Galaxy | 1909 |

Changeset 0:8be2feb96994 (2022-03-11)

Next changeset 1:5224b4d51065 (2022-03-11)

Commit message:
"planemo upload commit cb65588391944306ff3cb32a23e1c28f65122014"

EURL_VTEC_WGS_PT.py

diff -r 000000000000 -r 8be2feb96994 EURL_VTEC_WGS_PT.py

EURL_VTEC_WGS_PT.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/EURL_VTEC_WGS_PT.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,277 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+############################################################################
+# Istituto Superiore di Sanita'
+# European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
+# Developer: Arnold Knijn arnold.knijn@iss.it
+############################################################################
+"""
+
+import argparse
+import sys
+import os
+import shutil
+import subprocess
+import HTML
+import datetime
+import fileinput
+
+BASE_URL = 'https://aries.iss.it'
+TOOL_DIR = os.path.dirname(os.path.abspath(__file__))
+
+def insertFile(filename, report):
+    with open(filename) as html_in:
+        for line in html_in:
+            report.write(line)
+
+def insertFileAsTable(filename, report, hasheader=False, tabclass="table table-rep"):
+    with open(filename) as table_in:
+        table_data = [[str(col) for col in row.split('\t')] for row in table_in]
+    insertTable(table_data, report, hasheader, tabclass)
+
+def insertTable(table_data, report, hasheader=False, tabclass="table table-rep"):
+    if hasheader:
+        htmlcode = HTML.table(table_data[1:], attribs={'class':tabclass}, header_row=table_data[0])
+    else:
+        htmlcode = HTML.table(table_data, attribs={'class':tabclass})
+    report.write(htmlcode)
+
+def openFileAsTable(filename):
+    with open(filename) as table_in:
+        table_data = [[str(col).rstrip() for col in row.split('\t')] for row in table_in]
+    return table_data
+
+def __main__():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--serotyping', dest='serotyping', help='perform serotyping', action='store_true')
+    parser.add_argument('--virulotyping', dest='virulotyping', help='perform virulotyping', action='store_true')
+    parser.add_argument('--shigatoxintyping', dest='shigatoxintyping', help='perform shigatoxintyping', action='store_true')
+    parser.add_argument('--amrtyping', dest='amrtyping', help='perform amrtyping', action='store_true')
+    parser.add_argument('-1', '--input1', dest='input1', help='forward or single-end reads file in Sanger FASTQ format')
+    parser.add_argument('--input1_ext', dest='input1_ext', help='extension of forward or single-end reads file in Sanger FASTQ format')
+    parser.add_argument('--input1_name', dest='input1_name', help='name of forward or single-end reads file in Sanger FASTQ format')
+    parser.add_argument('-2', '--input2', dest='input2', help='reverse reads file in Sanger FASTQ format')
+    parser.add_argument('--input2_ext', dest='input2_ext', help='extension of reverse reads file in Sanger FASTQ format')
+    parser.add_argument('--input2_name', dest='input2_name', help='name of reverse reads file in Sanger FASTQ format')
+    parser.add_argument('--html1', dest='html1', help='html FASTQC file')
+    parser.add_argument('--html1_id', dest='html1_id', help='html FASTQC file id')
+    parser.add_argument('--html1_path', dest='html1_path', help='html FASTQC file path')
+    parser.add_argument('--text1', dest='text1', help='text FASTQC file')
+    parser.add_argument('--html2', dest='html2', help='html FASTQC file')
+    parser.add_argument('--html2_id', dest='html2_id', help='html FASTQC file id')
+    parser.add_argument('--html2_path', dest='html2_path', help='html FASTQC file path')
+    parser.add_argument('--text2', dest='text2', help='text FASTQC file')
+    parser.add_argument('--contigs', dest='contigs', help='Assembly contigs')
+    parser.add_argument('--quast', dest='quast', help='Quast report')
+    parser.add_argument('--log', dest='logfile', help='log file')
+    parser.add_argument('--virulotyper', dest='virulotyper', help='Virulotyping Mapping reads')
+    parser.add_argument('--virulotyper_id', dest='virulotyper_id', help='Virulotyping Mapping reads id')
+    parser.add_argument('--stx'..report.write("<p>Stx Subtypes: ")
+            if len(shigatoxin_typing) == 0:
+                str_shigatoxin_subtype = "No subtype match found"
+            else:
+                # get corresponding subtypes
+                str_shigatoxin_subtype = ""
+                shigatoxin_subtypes = []
+                shigatoxin_subtypes_raw = []
+                shigatoxin_types = openFileAsTable(TOOL_DIR + "/data/stx_subtypes")
+                for subtype in shigatoxin_typing:
+                    blast_pident_100 = float(subtype[1]) == 100
+                    if (blast_pident_100):
+                        for item in shigatoxin_types:
+                            if item[0] == subtype[0] and item[1] not in shigatoxin_subtypes_raw:
+                                shigatoxin_subtypes.append(item[1])
+                                shigatoxin_subtypes_raw.append(item[1])
+               # partial matches
+                for subtype in shigatoxin_typing:
+                    for item in shigatoxin_types:
+                        if item[0] == subtype[0] and item[1] not in shigatoxin_subtypes_raw:
+                            if item[1][0:4] == "stx1":
+                                shigatoxin_subtypes.append(item[1] + "(" + str(float(subtype[1])) + ")")
+                                shigatoxin_subtypes_raw.append(item[1])
+                            if item[1][0:4] == "stx2":
+                                shigatoxin_subtypes.append(item[1] + "(" + str(float(subtype[1])) + ")")
+                                shigatoxin_subtypes_raw.append(item[1])
+                shigatoxin_subtypes.sort()
+                str_shigatoxin_subtype = " ".join(shigatoxin_subtypes)
+            report.write("%s" % str_shigatoxin_subtype)
+            report.write("</p>\n")
+        # Quality Check
+        disclaimer = False
+        if any("-" in s for s in sequence_typing) or any("?" in s for s in sequence_typing):
+            disclaimer = True
+        if disclaimer:
+            report.write("<p style='font-weight:bold;color:red'>Disclaimer: The data analysed do not fulfill minimum quality parameters, please consider repeating the sequencing.</p>\n")
+        report.write("<hr/><h3>Raw data quality check</h3>\n")
+        if args.input2:
+            report.write("<p>FASTQC result forward: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html1_id))
+            report.write("<p>FASTQC result reverse: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html2_id))
+        else:
+            report.write("<p>FASTQC result: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.html1_id))
+        if args.serotyping:
+            report.write("<br/><hr/><h3>Serotyping</h3>\n")
+            insertFileAsTable("mmseqs_OH_fc", report, True)
+        report.write("<br/><hr/><h3>Multi Locus Sequence Typing</h3>\n")
+        if len(sequence_typing) > 1:
+            insertTable(sequence_typing, report, True)
+        if args.virulotyping:
+            report.write("<br/><hr/><h3>Virulotyping</h3>\n")
+            report.write("<p>This table is filtered for results with >90%% gene coverage, unfiltered results can be found <a href='%s/datasets/%s/display/?preview=True'>here</a></p>\n" % (BASE_URL, args.virulotyper_id))
+            insertFileAsTable("pathotyper_rep_tab", report, True, "table table-cross")
+        if args.shigatoxintyping:
+            report.write("<br/><hr/><h3>Shiga toxin typing</h3>\n")
+            insertFileAsTable(args.stx, report, True)
+        if args.amrtyping:
+            report.write("<br/><hr/><h3>AMR typing</h3>\n")
+            report.write("<p>AMR result: <a href='%s/datasets/%s/display/?preview=True'>Webpage</a></p>\n" % (BASE_URL, args.amr_id))
+        # write tail html
+        insertFile(TOOL_DIR + "/report_tail.html", report)
+    finally:
+        report.close()
+
+if __name__ == "__main__":
+    __main__()

HTML.py

diff -r 000000000000 -r 8be2feb96994 HTML.py

HTML.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/HTML.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,361 @@
+#!/usr/bin/python
+# -*- coding: iso-8859-1 -*-
+"""
+HTML.py - v0.04 2009-07-28 Philippe Lagadec
+
+This module provides a few classes to easily generate HTML code such as tables
+and lists.
+
+Project website: http://www.decalage.info/python/html
+
+License: CeCILL (open-source GPL compatible), see source code for details.
+         http://www.cecill.info
+"""
+
+__version__ = '0.04'
+__date__    = '2009-07-28'
+__author__  = 'Philippe Lagadec'
+
+#--- LICENSE ------------------------------------------------------------------
+
+# Copyright Philippe Lagadec - see http://www.decalage.info/contact for contact info
+#
+# This module provides a few classes to easily generate HTML tables and lists.
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use,
+# modify and/or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+#
+# A copy of the CeCILL license is also provided in these attached files:
+# Licence_CeCILL_V2-en.html and Licence_CeCILL_V2-fr.html
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and,  more generally, to use and operate it in the
+# same conditions as regards security.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+#--- THANKS --------------------------------------------------------------------
+
+# - Michal Cernoevic, for the idea of column styles.
+
+#--- REFERENCES ----------------------------------------------------------------
+
+# HTML 4.01 specs: http://www.w3.org/TR/html4/struct/tables.html
+
+# Colors: http://www.w3.org/TR/html4/types.html#type-color
+
+# Columns alignement and style, one of the oldest and trickiest bugs in Mozilla:
+# https://bugzilla.mozilla.org/show_bug.cgi?id=915
+
+
+#--- CONSTANTS -----------------------------------------------------------------
+
+# Table style to get thin black lines in Mozilla/Firefox instead of 3D borders
+#TABLE_STYLE_THINBORDER = "border: 1px solid #000000; border-collapse: collapse;"
+#TABLE_STYLE_THINBORDER = "border: 1px solid #000000;"
+
+
+#=== CLASSES ===================================================================
+
+class TableCell (object):
+    """
+    a TableCell object is used to create a cell in a HTML table. (TD or TH)
+
+    Attributes:
+    - text: text in the cell (may contain HTML tags). May be any object which
+            can be converted to a string using str().
+    - header: bool, false for a normal data cell (TD), true for a header cell (TH)
+    - bgcolor: str, background color
+    - width: str, width
+    - align: str, horizontal alignement (left, center, right, justify or char)
+    - char: str, alignment character, decimal point if not specified
+    - charoff: str, see HTML specs
+    - valign: str, vertical alignment (top|middle|bottom|baseline)
+    - style: str, CSS s..= self.cellpadding
+        for attr in self.attribs:
+            attribs_str += ' %s="%s"' % (attr, self.attribs[attr])
+        result = '<table%s>\n' % attribs_str
+        # insert column tags and attributes if specified:
+        if self.col_width:
+            for width in self.col_width:
+                result += '  <col width="%s">\n' % width
+        # First insert a header row if specified:
+        if self.header_row:
+            if not isinstance(self.header_row, TableRow):
+                result += str(TableRow(self.header_row, header=True))
+            else:
+                result += str(self.header_row)
+        # Then all data rows:
+        for row in self.rows:
+            if not isinstance(row, TableRow):
+                row = TableRow(row)
+            # apply column alignments  and styles to each row if specified:
+            # (Mozilla bug workaround)
+            if self.col_align and not row.col_align:
+                row.col_align = self.col_align
+            if self.col_char and not row.col_char:
+                row.col_char = self.col_char
+            if self.col_charoff and not row.col_charoff:
+                row.col_charoff = self.col_charoff
+            if self.col_valign and not row.col_valign:
+                row.col_valign = self.col_valign
+            if self.col_styles and not row.col_styles:
+                row.col_styles = self.col_styles
+            result += str(row)
+        result += '</table>'
+        return result
+
+
+#-------------------------------------------------------------------------------
+
+class List (object):
+    """
+    a List object is used to create an ordered or unordered list in HTML.
+    (UL/OL tag)
+
+    Attributes:
+    - lines: list, tuple or any iterable, containing one string for each line
+    - ordered: bool, choice between an ordered (OL) or unordered list (UL)
+    - attribs: dict, additional attributes for the OL/UL tag
+
+    Reference: http://www.w3.org/TR/html4/struct/lists.html
+    """
+
+    def __init__(self, lines=None, ordered=False, start=None, attribs=None):
+        """List constructor"""
+        if lines:
+            self.lines = lines
+        else:
+            self.lines = []
+        self.ordered = ordered
+        self.start = start
+        if attribs:
+            self.attribs = attribs
+        else:
+            self.attribs = {}
+
+    def __str__(self):
+        """return the HTML code for the list as a string"""
+        attribs_str = ""
+        if self.start:  self.attribs['start'] = self.start
+        for attr in self.attribs:
+            attribs_str += ' %s="%s"' % (attr, self.attribs[attr])
+        if self.ordered: tag = 'ol'
+        else:            tag = 'ul'
+        result = '<%s%s>\n' % (tag, attribs_str)
+        for line in self.lines:
+            result += ' <li>%s\n' % str(line)
+        result += '</%s>\n' % tag
+        return result
+
+#=== FUNCTIONS ================================================================
+
+# much simpler definition of a link as a function:
+def Link(text, url):
+    return '<a href="%s">%s</a>' % (url, text)
+
+def link(text, url):
+    return '<a href="%s">%s</a>' % (url, text)
+
+def table(*args, **kwargs):
+    'return HTML code for a table as a string. See Table class for parameters.'
+    return str(Table(*args, **kwargs))
+
+def list(*args, **kwargs):
+    'return HTML code for a list as a string. See List class for parameters.'
+    return str(List(*args, **kwargs))
+
+
+#=== MAIN =====================================================================
+
+# Show sample usage when this file is launched as a script.
+
+if __name__ == '__main__':
+
+    # open an HTML file to show output in a browser
+    f = open('test.html', 'w')
+
+    t = Table()
+    t.rows.append(TableRow(['A', 'B', 'C'], header=True))
+    t.rows.append(TableRow(['D', 'E', 'F']))
+    t.rows.append(('i', 'j', 'k'))
+    f.write(str(t) + '<p>\n')
+    print (str(t))
+    f.close()

LICENSE

diff -r 000000000000 -r 8be2feb96994 LICENSE

LICENSE

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,674 @@
+GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+  Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so.  This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software.  The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable.  Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products.  If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+  Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds..HE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.md

diff -r 000000000000 -r 8be2feb96994 README.md

EURL_VTEC_WGS_PT.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,21 @@
+# eurl_vtec_wgs_pt-galaxy
+ This tool performs various Escherichia coli typing tools and is implemented as a Galaxy (https://galaxyproject.org/) workflow
+
+    Raw data quality check (FASTQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+    Trimming (Trimmomatic, DOI:10.1093/bioinformatics/btu170)
+    Assembly (SPAdes, DOI:10.1089/cmb.2012.0021; SKESA, DOI:10.1186/s13059-018-1540-z)
+    Virulotyping (patho_typing tool from the INNUENDO Project)
+    Multi Locus Sequence Typing (MLST 7 loci, https://github.com/tseemann/mlst/)
+    Serotyping (MMseqs2, DOI:10.1038/s41467-018-04964-5)
+    Shigatoxintyping (blastn, DOI:10.1186/1471-2105-10-421, of a consensus sequence against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU, DOI:10.1128/JCM.00008-15)
+    AMR typing (AMRFinderPlus, DOI:10.1128/aac.00483-19)
+
+After installation the BASE_URL parameter in the EURL_VTEC_WGS_PT.py (line 20) will have to be modified to the url of your Galaxy instance in order to correctly visualise the FastQC results.
+
+The files duk, fastq_pair, stx_subtype_fa.sh, stx_subtype_pe.sh, stx_subtype_se.sh in the scripts folder and the file rematch.py in the scripts/ReMatCh folder should have execution rights.
+
+In order to make trimmomatic work, you will have to create the following symbolic link
+
+    cd /$GALAXY_DIR/tool_dependency_dir/_conda/envs/mulled-v1-9471dd12387e90c11124403c650a667dc2a8c932d610ab6fc4cf2e3f4b40720c/bin
+    chmod 755 ../share/trimmomatic-0.39-1/trimmomatic.jar
+    ln -s ../share/trimmomatic-0.39-1/trimmomatic.jar trimmomatic.jar

data/H_type.fsa

diff -r 000000000000 -r 8be2feb96994 data/H_type.fsa

data/H_type.fsa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/H_type.fsa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,2377 @@
+>fliC_307_AY249994_H9
+ATGGCACAAGTCATTAATACCAACAGCCTCTCGCTGATCACTCAAAATAATATCAACAAGAACCAGTCTGCG
+CTGTCGAGTTCTATCGAGCGTCTGTCTTCTGGCTTGCGTATTAACAGCGCGAAGGATGACGCCGCGGGTCAG
+GCGATTGCTAACCGTTTTACTTCTAACATTAAAGGCCTGACTCAGGCTGCACGTAACGCCAACGACGGTATT
+TCCGTTGCACAGACCACTGAAGGCGCGCTGTCCGAAATTAACAACAACTTACAGCGTATTCGTGAACTGACG
+GTTCAGGCTTCTACCGGGACTAACTCCGATTCGGATCTGGACTCCATTCAGGACGAAATCAAATCCCGTCTG
+GACGAAATTGACCGCGTATCCGGCCAGACCCAGTTCAACGGCGTGAACGTGCTGTCCAAAGATGGCTCGATG
+AAAATTCAGGTCGGCGCGAACGATGGCGAAACGATTACTATTGATCTGAAGAAAATTGACTCTGATACGCTG
+AATCTGGCTGGTTTTAACGTTAACGGTAAAGGTTCTGTAGCGAATACAGCTGCGACAAGCGACGATTTAAAA
+CTGGCTGGTTTCACTAAGGGCACCACAGATACCAATGGCGTGACCGCGTATACAAACACAATTAGTAATGAC
+AAAGCCAAAGCTTCCGATCTGTTAGCTAATATCACCGATGGATCAGTGATCACTGGGGGAGGGGCAAACGCT
+TTTGGCGTGGCTGCAAAGAATGGTTACACCTATGATGCAGCAAGTAAATCTTATAGTTTTGCTGCAGATGGT
+GCCGATTCAGCGAAGACGTTAAGCATCATTAATCCAAACACCGGTGATTCGTCGCAGGCGACAGTGACTATT
+GGTGGTAAAGAGCAGAAAGTTAATATTTCCCAGGATGGAAAAATTACTGCGGCAGATGATAATGCGACGCTG
+TATTTAGATAAACAGGGAAACTTGACAAAAACGAATGCAGGTAACGATACCGCAGCGACTTGGGATGGTTTA
+ATTTCCAACAGCGATTCTACCGGTGCGGTTCCAGTTGGGGTTGCAACTACAATTACAATTACTTCTGGTACA
+GCTTCCGGAATGTCTGTTCAGTCCGCAGGAGCAGGAATTCAGACCTCAACAAATTCTCAGATTCTTGCAGGT
+GGTGCATTTGCGGCTAAGGTAAGTATTGAGGGAGGCGCTGCTACAGACATTTTGGTAGCAAGTAATGGAAAC
+ATAACAGCGGCTGATGGTAGTGCACTTTATCTTGATGCGACTACTGGTGGATTCACTACAACGGCTGGAGGA
+AATACAGCTGCTTCGTTAGATAATTTAATTGCTAACAGTAAGGATGCTACCTTAACCGTAACTTCAGGTACC
+GGCCAGAACACTGTTTATAGCACAACAGGAAGTGGCGCTCAGTTCACCAGTTTAGCAAAAGTAGACACAGTC
+AATGTCACCAACGCACATGTCAGTGCCGAAGGTATGGCAAATCTGACAAAAAGCAATTTTACCATTGATATG
+GGCGGTACAGGTACAGTAACTTACACAGTTTCCAATGGGGATGTGAAAGCTGCTGCAAATGCTGATGTTTAT
+GTCGAAGATGGTGCACTTTCAGCCAATGCTACAAAAGATGTAACCTACTTTGAACAAAAAAATGGGGCTATT
+ACCAACAGCACCGGTGGTACCATCTATGAAACAGCTGATGGTAAGTTAACAACAGAAGCTACTACTGCATCC
+AGTTCCACCGCCGATCCCCTGAAAGCTCTGGACGAAGCCATCAGCTCCATCGACAAATTCCGCTCCTCCCTC
+GGTGCGGTGCAAAACCGTCTGGATTCCGCGGTCACCAACCTGAACAACACCACTACCAACCTGTCCGAAGCG
+CAGTCCCGTATTCAGGACGCCGACTATGCGACCGAAGTGTCCAACATGTCGAAAGCGCAGATCATCCAGCAG
+GCCGGTAACTCCGTGCTGGCAAAAGCTAACCAGGTACCGCAGCAGGTTCTGTCTCTGCTGCAGGGTTAA
+>fliC_52_AJ605764_H4
+ATGGCACAAGTCATTAATACCAACAGCCTCTCGCTGATCACTCAGAACAACATCAACAAAAACCAGTCTGCG
+CTGTCGACTTCTATCGAGCGCCTCTCTTCTGGTCTGCGTATTAACAGCGCTAAAGATGACGCCGCGGGCCAG
+GCGATTGCTAACCGCTTTACTTCTAACATCAAAGGTCTGACTCAGGCCGCACGTAACGCCAACGACGGTATT
+TCTCTGGCGCAGACGGCTGAAGGCGCGCTGTCAGAGATTAACAACAACTTGCAGCGTATTCGTGAACTGACC
+GTTCAGGCCTCTACCGGCACGAACTCTGATTCCGACCTGTCTTCTATTCAGGACGAAATCAAATCCCGTCTT
+GATGAAATTGACCGTGTATCTGGTCAGACCCAGTTCAACGGTGTGAACGTGCTGTCGAAAAACGATTCGATG
+AAGATTCAGATTGGTGCCAATGATAACCAGACGATCAGCATTGGCTTGCAACAAATCGACAGTACCACTTTG
+AATCTGAAAGGATTTACCGTGTCCGGCATGGCGGATTTCAGCGCGGCGAAACTGACGGCTGCTGATGGTACA
+GCAATTGCTGCTGCGGATGTCAAGGATGCTGGGGGTAAACAAGTCAATTTACTGTCTTACACTGACACCGCG
+TCTAACAGTACTAAATATGCGGTCGTTGATTCTGCAACCGGTAAATACATGGAAGCCACTGTAGTCATTACC
+GGTACGGCGGCGGCGGTAACTGTTGGTGCAGCGGAAGTGGCGGGAGCCGCTACAGCCGATCCGTTAAAAGCA
+CTGGATGCCGCAATCGCTAAAGTCGACAAATTCCGCTCCTCCCTCGGTGCCGTTCAAAACCGTCTGGATTCT
+GCGGTCACCAACCTGAACAACACCACCACCAACCTGTCTGAAGCGCAGTCCCGTATTCAGGACGCCGACTAT
+GCGACCGAAGTGTCCAACATGTCGAAAGCGCAGATTATCCAGCAGGCGGGCAACTCCGTGCTGTCTAAAGCC
+AACCAGGTACCGCAGCAAGTTCTGTCTCTGTTACAAGGCTAA
+>fliC_51_AJ536600_H4
+ATGGCACAAGTCATTAATACCAACAGCCTCTCGCTGATCACTCAGAACAACATCAACAAAAACCAGTCTGCG
+CTGTCGACTTCTATCGAGCGCCTCTCTTCTGGTCTGCGTATTAACAGCGCTAAAGATGACGCCGCGGGCCAG
+GCGATTGCTAACCGCTTTACTTCTAACATCAAAGGTCTGACTCAGGCCGCACGTAACGCCAACGACGGTATT
+TCTCTGGCGCAGACGGCTGAAGGCGCGCTGTCAGAGATTAACAACAACTTGCAGCGTATTCGTGAACTGACC
+GTTCAGGCCTCTACCGGCACGAACTCTGATTCCGACCTGTCTTCTATTCAGGACGAAATCAAATCCCGTCTT
+GATGAAATTGACCGTGTATCTGGTCAGACCCAGTTCAACGGTGTGAACGTGCTGTCGAAAAACGATTCGATG
+AAGATTCAGATTGGTGCCAATGATAACCAGACGATCAGCATTGGCTTGCAACAAATCGACAGTACCACTTTG
+AATCTGAAAGGATTTACCGTGTCCGGCATGGCGGATTTCAGCGCGGCGAAACTGACGGCTGCTGATGGTACA
+GCAATTGCTGCTGCGGATGTCAAGGATGCTGGGGGTAAACAAGTCAATTTACTGTCTTACACTGACACCGCG
..AAAACCGTTGCTAATGGCGGTGAT
+ATCGTTCTGTCCTCTAAAACTATTAAAGCAGAAATCCAGATTGATAGTCATAGTGCTGATCCAAAAGCGGCA
+GACGGTTTGTATGCATTGAAGGATGGTACCGGATATGCAGTAAAAGATAAAGACGGTGCATATCACGCTGCT
+GTTAAAAATGCTGATGGTAAGGTCACTTGGGATTCAAGTGATACTTCTGTGACAGCAACTGATGTTGACCAA
+ACCACAAAGGTTACAGAATTCCAGGAAGTATATAAAAAGGTTGCAGCAAATACATCTGGACTTGCTGCTAAC
+CAAACATTTAAATCTTACAAAAAAGATAATGGCGAACTTGGATATGTGGTTGAAAACGCTGATGGCACTTTT
+AACCGTGCTAACGTCGATTCAAAAACGGGTGTTGTTTCTGTAGGAACTAAAATTTCCACAAGCCCTGATGTT
+TTAGCAACTATCGATAATGCTTTGAAGATTGTTGACTCTCAACGTAGCTCTTTAGGTGCCATCCAGAACCGT
+TTCGATTCGGCCATCACTAACTTGGGTAACACAGTGAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGAC
+TCCGACTACGCGACCGAAGTGTCTAACATGTCTCGTGCACAGATCCTGCAACAAGCGGGTACTTCTGTTCTG
+GCACAAGCAAACCAGACGACCCAGAACGTACTGTCTCTTCTGCGTTAA
+>flkA_3_EF392692_H35
+ATGGCACAAGTTATCAATACCAACAGCCTGTCGCTGTTGACTCAAAATAACCTGAATAAATCACAGTCCTCT
+CTGAGTTCGGCTATTGAACGTCTGTCTTCTGGTTTGCGTATCAACAGCGCTAAAGACGACGCAGCAGGTCAG
+GCGATTGCTAACCGCTTTACTTCAAACATTAAGGGCCTGACCCAGGCATCTCGTAATGCCAATGATGGGATT
+TCTGTAGCTCAGACGACCGAAGGTTCATTATCTGAAATCAACAATAACTTACAGCGTATTCGTGAGTTGTCA
+GTACAAGCAACTAATGGCTCTAACTCTGATTCAGACTTGTCCTCGATTCAGGATGAGATTACTCAACGTTTG
+CAAGAAATTGATCGTGTCTCCAATCAGACTCAGTTTAACGGCGTAAAAGTATTAGCATCTCAACAGACTATG
+AAAATTCAGGTTGGTGCTAACGACGGCGAAACAATTACGATTGATTTAAAAGAAATTAATAGCAAAACTTTG
+GGATTGGATAAATTAGATGTGCGTAACACATTTAGCACATCTGATCTAGCTGCAACTGCAACTACTGAACTA
+GCTCCGGCTAAAACAGATGTTAAAAATCTGACGTTTACTGATGGCGCAACAGCTCCTACATTTAAGTTGTAC
+GTTGATAATACAGATCCTGACAAATTATTCGTTTCTTCAAATGGTACCAACTATTACGCTGCTAGTTACGAT
+AAAGACACAAACTCTATTAAGTTTAACTCCACAGGTACTGGTACTACAGGTACAGCGGGAACCGATTTTATT
+GACGCGACCGGTAAAGATGTCCATGTGGGTGGTGGACGTGTAATGGCTGCAAATGATATCAAAGGCCGTACA
+GATGACAATGTAGCTGCTAAGCCTCAACTTTTCTTAGACCAGAGCGGTAAGTATCATATCAGTAAAGATAAT
+GGTGCAACCTATGCTAATGCAACTGTGAATGCCACTACTGGCGAAGTAACCTACGATTCCGGAACAGCGGCT
+GCCCTTGGTGCTGGTATTGAAGTTGGTAGCGCACTTAAAGAGATTGCTAAACCAGACGCTGGGGTGGCTGTG
+GACCTTACTGGTGTTTCTGGTGTTACAGGTGCACAATTATTCGCGAAAAAGGATGGTAGCGGTTATGTAATT
+AAAGGCACTGCTGATAATAAAGAAGTACTGTTCGAAGCAAAAGTTGCTGCTGATGGCAAAGTGACTAAGGGT
+GATCAACTTACAGCAGATCCCCTTAAAAGTATTGATGATGCACTTTCCCAAGTGGATCAATTCCGTAGCTCC
+TTGGGGGCAGTGCAAAACCGCTTCGATTCTGCTATCACTAACTTAGGTAATACTGTAAACAATCTGTCTTCT
+GCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTATCTAACATGTCTCGTGCACAGATCCTGCAA
+CAGGCAGGTACTTCTGTTCTGGCGCAGGCTAACCAGACAACTCAGAACGTACTGTCTCTTCTGCGTTGA
+>flkA_4_AB128916_H3
+ATGGCACAAGTTATCAATACCAACAGCCTGTCGCTGTTGACTCAAAATAACCTGAATAAATCACAGTCTTCT
+CTGAGTTCGGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGTGCGAAAGACGATGCAGCAGGCCAG
+GCGATTGCTAACCGCTTCACATCTAACATCAAGGGGTTAAGCCAGGCATCTCGTAATGCTAATGATGGTATC
+TCACTGGCACAGACCACTGAAGGTGCACTGTCAGAAATCAACAACAACCTCCAACGAGTACGTGAGCTTGCT
+GTTCAGGCTACTAACGGCACGAACTCTCAGTCTGATCTAAACTCCATTCAAGACGAAATTACTCAGCGCCTG
+AGTGAAATTGATCGTGTTTCTCAACAGACTCAATTCAATGGTGTAAAAGTATTGGCAACTAACCAAACGATG
+AAAATTCAGGTTGGCGCAAATGACGGTCAGACTATAGAAATTGGATTAGATAAAATTGATGCAGACACTCTC
+GGTCTGAAAGACTTTAGCGTAGCATCTGCAAAAGTGCCTACATCAGGAGCGGTTGCATTAAAAAGTGAAATG
+TCTCCAACATTAACCTCTGTAAATGCAACTACTGGTAAAAATGGTACTAACTACGCATTTGGAGCTACATTC
+CGCACTGATGATGTTAATACTTATTTTGGCGGAAAAGCTGTTAATACTGGTGATAAAACAAATGTATTAGGC
+ACAGAGGCGGAAGTATTCCAGATTCAGGTTGAAGGACAAACCTACTTTGTAGCACAAAATGGAGATACTGCC
+ACTAATGCTTATTCCTTACTTAAGCAATCTGGTTCAGGTTATGAAAAAGTAACTGTTGATAGTAAAGCTGTT
+CAGATTGCGAATTTTGGCGGGCGAGTTACAGCATTTGTTGACGATGGTACCGCTGCTCATAACGCTCTTTCT
+GTTGATCTACAGAAAGGAACTGTTGGAAAAGCATTATCTTTCAACGATTCTCAGATGTCAGTATATGTTGAC
+GGTAAAAACCTTGAAATTAAGCAGGTTCTGGACGCTGATGGTAAGCCTAAAGCAGGTGCTTTTGCAGCTCAA
+ACCGCTGATGGTAAGTCTTTAGCTGTCAATATTGATGGCAACGGCAATACTTCTGTTGTGAAAGATGCAGAC
+GGCAATAATGTCGAATGGGTTGTTGATAAAGACGGTGCAGCTAAGACTGTTGTACGTAAAGATGACAAAATA
+TACGGCGCTTCAGTAACAGGGTTTGGTGGGACTCCAACTGTTAACGTTGATACAACCGCAATTGATGCTTCT
+GAGTTAAAAGGCATGACAACTGCTAAGCCACTGGAAAAATTAGATACAGCTTTAGCTAAAGTTGATAAGTTG
+CGCAGCTCCCTTGGTGCGGTACAGAACCGTTTTGATTCTGCTATTACCAACTTGGGTAATACTGTTAACAAC
+CTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACTGAAGTATCTAACATGTCTCGTGCACAG
+ATCCTGCAGCAGGCGGGTACTTCTGTTCTGGCACAGGCTAACCAGACCACGCAGAACGTACTGTCTCTTCTG
+CGTTAA
\ No newline at end of file

data/H_type.nhr

diff -r 000000000000 -r 8be2feb96994 data/H_type.nhr

data/H_type.nhr

Binary file data/H_type.nhr has changed

data/H_type.nin

diff -r 000000000000 -r 8be2feb96994 data/H_type.nin

data/H_type.nin

Binary file data/H_type.nin has changed

data/H_type.nsq

diff -r 000000000000 -r 8be2feb96994 data/H_type.nsq

data/H_type.nsq

Binary file data/H_type.nsq has changed

data/H_typeDB

diff -r 000000000000 -r 8be2feb96994 data/H_typeDB

data/H_typeDB

Binary file data/H_typeDB has changed

data/H_typeDB

diff -r 000000000000 -r 8be2feb96994 data/H_typeDB.dbtype

data/H_typeDB

Binary file data/H_typeDB.dbtype has changed

data/H_typeDB

diff -r 000000000000 -r 8be2feb96994 data/H_typeDB.index

data/H_typeDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/H_typeDB.index Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,102 @@
+0 0 2015
+1 2015 1469
+2 3484 1760
+3 5244 1727
+4 6971 1052
+5 8023 1478
+6 9501 1760
+7 11261 1673
+8 12934 1052
+9 13986 1655
+10 15641 1760
+11 17401 1109
+12 18510 1052
+13 19562 1676
+14 21238 1760
+15 22998 1274
+16 24272 1052
+17 25324 1676
+18 27000 1760
+19 28760 1511
+20 30271 1052
+21 31323 1481
+22 32804 1721
+23 34525 1592
+24 36117 1265
+25 37382 1667
+26 39049 1760
+27 40809 1265
+28 42074 1496
+29 43570 1760
+30 45330 1346
+31 46676 1682
+32 48358 1760
+33 50118 1346
+34 51464 1481
+35 52945 1760
+36 54705 1301
+37 56006 1499
+38 57505 1760
+39 59265 1283
+40 60548 1481
+41 62029 1760
+42 63789 1283
+43 65072 1655
+44 66727 1760
+45 68487 1313
+46 69800 1670
+47 71470 1844
+48 73314 1313
+49 74627 1835
+50 76462 1697
+51 78159 1313
+52 79472 1670
+53 81142 1700
+54 82842 1334
+55 84176 1691
+56 85867 1790
+57 87657 1325
+58 88982 1709
+59 90691 1790
+60 92481 1325
+61 93806 1688
+62 95494 1742
+63 97236 1334
+64 98570 1580
+65 100150 1790
+66 101940 1289
+67 103229 1580
+68 104809 1715
+69 106524 1346
+70 107870 1577
+71 109447 1790
+72 111237 1346
+73 112583 1580
+74 114163 1790
+75 115953 1346
+76 117299 1577
+77 118876 1742
+78 120618 1499
+79 122117 1577
+80 123694 1790
+81 125484 1463
+82 126947 1760
+83 128707 1769
+84 130476 1508
+85 131984 1760
+86 133744 1820
+87 135564 1640
+88 137204 1715
+89 138919 1820
+90 140739 1640
+91 142379 1760
+92 144139 1484
+93 145623 1649
+94 147272 1760
+95 149032 1526
+96 150558 1469
+97 152027 1715
+98 153742 1553
+99 155295 1649
+100 156944 1733
+101 158677 1871

data/H_typeDB

diff -r 000000000000 -r 8be2feb96994 data/H_typeDB.lookup

data/H_typeDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/H_typeDB.lookup Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,102 @@
+0 fliC_307_AY249994_H9 0
+1 fliC_276_AY337472_H11 0
+2 fliC_25_AB334574_H7 0
+3 fllA_2_AB269770_H44 0
+4 fliC_52_AJ605764_H4 0
+5 fliC_84_AIHL01000060_H21 0
+6 fliC_24_AF228496_H7 0
+7 flkA_2_EF392693_H36 0
+8 fliC_51_AJ536600_H4 0
+9 fliC_82_AIFA01000047_H6 0
+10 fliC_23_AF228495_H7 0
+11 flkA_1_EF392694_H47 0
+12 fliC_54_AJ605766_H17 0
+13 fliC_26_AY250008_H26 0
+14 fliC_94_AY337468_H7 0
+15 flkA_5_AB128917_H53 0
+16 fliC_53_AJ605765_H4 0
+17 fliC_285_AY337483_H26 0
+18 fliC_95_JH694260_H7 0
+19 flkA_3_EF392692_H35 0
+20 fliC_50_AJ515904_H17 0
+21 fliC_55_AJ884568_H40 0
+22 fliC_96_AY250024_H46 0
+23 flkA_4_AB128916_H3 0
+24 fliC_284_AY337482_H10 0
+25 fliC_308_AY250001_H18 0
+26 fliC_97_KB000721_H7 0
+27 fliC_33333_AY249995_H10 0
+28 fliC_85_AIHA01000023_H2 0
+29 fliC_98_AB334575_H7 0
+30 fliC_44444_AY250028_H52 0
+31 fliC_13_AY250020_H41 0
+32 fliC_99_KB007180_H7 0
+33 fliC_888881_AVRH01000047_H52 0
+34 fliC_86_AJ865465_H8 0
+35 fliC_100_AOES01000098_H7 0
+36 fliC_55555_AY250019_H39 0
+37 fliC_87_AF543692_H2 0
+38 fliC_15_AF228487_H7 0
+39 fliC_274_AY337470_H42 0
+40 fliC_56_AJ884569_H8 0
+41 fliC_108_KB006714_H7 0
+42 fliC_1111111_AY250021_H42 0
+43 fliC_89_AY249998_H14 0
+44 fliC_101_JH946604_H7 0
+45 fliC_7777777_AY249990_H5 0
+46 fliC_314_CP000247_H31 0
+47 fliC_102_AY250002_H19 0
+48 fliC_22222222_AY250029_H56 0
+49 fliC_282_AY337479_H19 0
+50 fliC_103_AY250026_H49 0
+51 fliC_273_AY337469_H5 0
+52 fliC_313_AY250013_H31 0
+53 fliC_5_AB028480_H49 0
+54 fliC_311_AGSG01000116_H25 0
+55 fliC_306_AY249999_H15 0
+56 fliC_303_L07387_H1 0
+57 fliC_111197_JH965342_H29 0
+58 fliC_90_AY250023_H45 0
+59 fliC_104_AB028471_H1 0
+60 fliC_286_AY337485_H29 0
+61 fliC_91_AY250017_H37 0
+62 fliC_105_AAJT02000052_H28 0
+63 fliC_999999_AY250012_H29 0
+64 fliC_279_AY337475_H16 0
+65 fliC_83_AIFX01000055_H12 0
+66 fliC_444444_AY250015_H33 0
+67 fliC_280_AY337476_H16 0
+68 fliC_3_AB028478_H46 0
+69 fliC_270_AY337466_H38 0
+70 fliC_92_JH954529_H16 0
+71 fliC_275_AY337471_H12 0
+72 fliC_277_AY337473_H38 0
+73 fliC_281_AY337477_H16 0
+74 fliC_278_AY337474_H12 0
+75 fliC_5555_AY250018_H38 0
+76 fliC_93_JH953794_H16 0
+77 fliC_88_AY250010_H28 0
+78 fliC_H48_AY250025_H48 0
+79 fliC_300_AB128919_H16 0
+80 fliC_77_AB028475_H12 0
+81 fliC_109_AM231154_H27 0
+82 fliC_22_AF228494_H7 0
+83 fliC_81_AB028476_H23 0
+84 fliC_110_AIGA01000038_H43 0
+85 fliC_19_AF228491_H7 0
+86 fliC_66_AY250027_H51 0
+87 fliC_317_AF345850_H34 0
+88 fliC_40_AY250014_H32 0
+89 fliC_6_AB028481_H51 0
+90 fliC_318_AY250016_H34 0
+91 fliC_20_AF228492_H7 0
+92 fliC_111_OwnSeqTestStrain_H24 0
+93 fliC_1_AY249991_H6 0
+94 fliC_21_AB028474_H7 0
+95 flnA_2_CP002291_H17 0
+96 fliC_269_AY337465_H11 0
+97 fliC_312_AY250011_H30 0
+98 flmA_1_AB128918_H54 0
+99 fliC_2_AIEY01000041_H6 0
+100 fliC_309_AY250003_H20 0
+101 fllA_1_AB269771_H55 0

data/H_typeDB

diff -r 000000000000 -r 8be2feb96994 data/H_typeDB_h

data/H_typeDB

Binary file data/H_typeDB_h has changed

data/H_typeDB

diff -r 000000000000 -r 8be2feb96994 data/H_typeDB_h.dbtype

data/H_typeDB

Binary file data/H_typeDB_h.dbtype has changed

data/H_typeDB

diff -r 000000000000 -r 8be2feb96994 data/H_typeDB_h.index

data/H_typeDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/H_typeDB_h.index Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,102 @@
+0 0 23
+1 23 24
+2 47 22
+3 69 22
+4 91 22
+5 113 27
+6 140 22
+7 162 22
+8 184 22
+9 206 26
+10 232 22
+11 254 22
+12 276 23
+13 299 23
+14 322 22
+15 344 22
+16 366 22
+17 388 24
+18 412 22
+19 434 22
+20 456 23
+21 479 23
+22 502 23
+23 525 21
+24 546 24
+25 570 24
+26 594 22
+27 616 26
+28 642 26
+29 668 22
+30 690 26
+31 716 23
+32 739 22
+33 761 31
+34 792 22
+35 814 27
+36 841 26
+37 867 22
+38 889 22
+39 911 24
+40 935 22
+41 957 23
+42 980 28
+43 1008 23
+44 1031 23
+45 1054 27
+46 1081 24
+47 1105 24
+48 1129 29
+49 1158 24
+50 1182 24
+51 1206 23
+52 1229 24
+53 1253 22
+54 1275 28
+55 1303 24
+56 1327 21
+57 1348 27
+58 1375 23
+59 1398 23
+60 1421 24
+61 1445 23
+62 1468 28
+63 1496 27
+64 1523 24
+65 1547 27
+66 1574 27
+67 1601 24
+68 1625 22
+69 1647 24
+70 1671 23
+71 1694 24
+72 1718 24
+73 1742 24
+74 1766 24
+75 1790 25
+76 1815 23
+77 1838 23
+78 1861 24
+79 1885 24
+80 1909 23
+81 1932 24
+82 1956 22
+83 1978 23
+84 2001 28
+85 2029 22
+86 2051 23
+87 2074 24
+88 2098 23
+89 2121 22
+90 2143 24
+91 2167 22
+92 2189 32
+93 2221 21
+94 2242 22
+95 2264 22
+96 2286 24
+97 2310 24
+98 2334 22
+99 2356 25
+100 2381 24
+101 2405 22

data/O_type.fsa

diff -r 000000000000 -r 8be2feb96994 data/O_type.fsa

data/O_type.fsa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/O_type.fsa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,1026 @@
+>wzx_1_GU299791_O1
+GTGAGCAAAAGTGAAATAAGGAACGTAATCCACAATGCTGGCTATATGATGATTACTCAGATAGCTTTATATGTTGCACCATTATTTATACTGAGTTATCTGTTAAAAACACTGGGGGTTGCACAGTTTGGTAATTATGCCTTAATACTATCAATCGTTGCATATTTACAGATTATAACGGATTATGGTTTTTCTTTTAGTGCAAGTCGTGCGATCTCACAGAATAGAGAGGACAAAGAATATATATCAAAAATTTATCTGTCAACTATGACTATCAAGTTGGCGATATGCGCTTTCTTATTCTTATTGCTCATGCTATTTTTAAATCTTTTGCCTGTGCAAGCTGAATTAAAACAAGGAATATTATATGGATATCTTCTTGTAATAGGAAATACTTTCCAACCACAATGGTTTTTCCAAGGTATCGAAAAATTAAAAATCATAGCCCTTTCTAATGTTATATCAAGATGCGCCGCGTGTTTACTTGTATTTATCTATGTGAGGAATAGCGAGGATTTACAAAAAGCACTTTTAGTACAGTCACTTCCATTAGTAATTTCTGCGATTGGATTAAATATATTTATATTGAAATATATCAATATTATTTTTCCGGAAAAAAAATTATTTAAGGTAATTTTAAAAGAAGGTAAGGATTTTTTTCTTGCATCACTTTATTCTGTTATTCTCAATAATAGTGGCATTTTTCTATTAGGGATTTTTACTAATCCTGTTATTGTTGGTGTATATGCCGCCGCTGAAAAGATAGTCAAGGCCGTATTGTCGCTATTTACACCACTGACGCAAGCTATATATCCTTATAATTGTCGTAAGTTTTCACTATCCGTATTTGACGGCATTGAGGCAGCAAAAAAAACTGGTATACCAATTATAATTTTAGCATTTATAGCTGCTGTTATCGTTGCAATTACCTTACCTGTTGCAATCGACTATCTTAATTTTCCAAAAGAAACAATTTTTGTAGGTCAAATATTAAGTGCATGGATCTTTTTTGGTGTTCTTAATAATGTATTCGGCATTCAGATATTGAGTGCATCAGGAAGAAGTAAAATATATAGTAGGATGGTATTCGTATCAGCGCTTATAACATTACTTTTGATTACTCTATTATTGCAGTTTTGTAACGCCACTGGAGTGGCATGTGCAATATTATTGGGTGAAATGTTCTTATCAATATTGTTACTTAAGCGATATAAAAAAATAATTTAA
+>wzx_5_EU694097_O3
+ATGCATGTTCGGGTTGCTGTAAATTTTGCATCAAAGATAACATTTGCTTTGATATCTATAATTACAATTCCAGTTATAAAATCAAAATTAGGAGTAAATGCTTATGGTGTCCTAACATTCTTTCTATCAATCCAGGTAGTTATATTACTGCTTGAGGGGGGAATGAGTGCCACAATGGCTAGAGGACTATTGAATAAAAAATATAAGATATACAATATAAGTAAAGCAGAGTACCAAAGTGTTTATTTTATCTTTTTTATATTAGTGTCATTATTTGTATTTTCAATTTTTATTGTCTTTAATCATAATATTTCCACATTGATTTACAACCTTGATGATAGGGAAGTCTATAGTTTTATTAGTGCTGATTATGTTATTTTGCTGGCTGGTGCAATGATTGCCTTGCAGTTTTATATCATATATTATGAAGCATTATTTGTGGCTTATGAAAAACAAGTCTCTTATGGAATTCATATAATAGTATTTAATGTAATCAAAACCATAATATCATTGTTCTTGTTGATTGTCTTTAATCTTGGGTTGGATGTTTATTTTTTAGTTCATGTATTTTGTACCTTTATACTTATTATTTTATTGCACATTAAGGCAATAAAAAACGGATTATTAGAAATAACAACATTGCGAGTGAAAAAAATATACACAAAAATATCATTTATGAAAGAAGAATTTCATTTTTCTAAAAATATATTATGCGTGTCCATTCTTTCTGCAATTGCATTCCAAGCTGACAGACTATTTATTACAAAATATATGGGTATTAGTGCTGTTGGAATGTATGGTATTGCTTATACATTATCAACAGTACCAACTTTATTTACATCATCATTGTATAATGTTATCTATCCAAGACTTATTATTTTAACAAGAGAGCAAAGCAGCAGTGCGATTTCATTTTTTGAATTAGTATCGAAATTAATATATATTATCATAATACCCACTTGTGTGATTATTTCGCTTAATTCGACCCAAATCCTAAATATTTGGATAGGAAAGCACGAAGGAATAATATCATTGCTGTTAAGTATTCTAATAATAGCGACGTTATTTCAGGGGTTGCAGGTGATTCCTTTTGCACTACAGATGGCTCAAGAACGACTAAAATTTACAGTTTTCATGAATGCTATATTTGTGCCCAGCCTAATATTGGCATATTATTTGGTTAGTATTCATAAAATTCTGTTATACATCTCCATAGTGTGGTCAGTATATAATATAATAACTTTTTTCTCTTTAACTATTTATTTATATGCTAAAAATAAAATGTATACAAGACTACTTATTTTATATTTTAATATATGCTTGTGTGCTGTCGTAACAGTAGTTATATGTAGCATTTTTAAGAATCAAGAATCTCAAATATTCTTGTCTCTAGTTAATATTTCTCTTCAGTTTTTTATGTCGATGAGTTTGTGCATAATACTGTTGTTCTGGAAAACTATATATGGAGCATTGAGATGTGTTTGTTGTCGGTAG
+>wzx_7_AY568960_O4
+ATGAGTTTAATTAGAAACAGTTTCTATAATATTGCTGGTTTTGCTGTGCCGACATTAGTTGCAGTCCCTGCTTTGGGGATTCTTGCCAGGCTGCTTGGACCGGAGAATTTTGGACTTTTCACACTAGCATTCGCTTTGATAGGATATGCAAGTATTTTCGACGCCGGGATTAGTCGAGCTGTAATCAGAGAAATCGCTCTTTATCGAGAAAGTGAAAAAGAGCAAATACAAATTATTTCGACAGCAAGTGTAATCGTACTATTCTTAGGGGTGGTTGCAGCTTTGTTACTTTATTTTAGTAGTAATAAAGTTGTTGAGTTATTGAATGTTAGTTCCGTTTATATTGAAACAGCAGTGCGTGCATTCTCTGTTATTTCATTTATAATACCTGTGTATCTGATTAACCAGATTTGGCTTGGTTATCTGGAAGGGCTAGAAAAATTTGCAAATATAAATGTTCAGAGAATGATTTCTAGCACAAGCTTGGCTATATTACCAGTGATATTTTGTTATTACAATCCCTCGTTGCTTTATGCTATGTATGGGTTGGTGGTTGGGCGTGTGATTTCATTTTTGATTAGCGCAATAATTTGTCGAGATATTATTCTTAAAAGTAAACTTTACTTTAATGTGGCAACTTGCAATCGTCTTATCTCTTTTGGTGGATGGATAACAGTTAGTAATATCATAAGCCCAATCATGGCATATTTCGACCGCTTTATCATCTCTCATATTATGGGGGCTTCGAGAATTGCATTTTATACAGCGCCCTCAGAGGGTGTATCAAGGTTAATTAATATCCCATATGCTTTGGCAAGAGCTCTATTTCCTAAATTGGCATATAGCAATAATGATGATGAACGAAAAAAATTACAACTACAGAGCTACGCAATTATAAGCATTGTATGTCTACCCATAGTTGTTATTGGTGTCATTTTTGCCTCATTCATAATGACAACATGGATGGGACCTGATTATGCCTTAGAAGCAGCAACTATCATGAAAATACTTCTTGCTGGTTTTTTCTTTAACTCTTTAGCGCAAATACCTTATGCATACTTGCAATCTATCGGAAAGTCAAAAATTACCGCATTTG..TAGAGTCTCGAAGAGACTATGTTTTTTTTAATGCTGGCTTTATTGCAATAACTTTACTGCTCTTAAGCTATCAGGTTGATATTTTGTTTAGATTTTTCTCTTTTTTTGAGACTTCATTTGTCTTGTTGTACTGCATTATTTTTTCTGGTTTTAATAAAAAAAGTAAAATTATACTGCATATGGTTAATTTAATTGTATATACGGTAATGACATTTAACATGTTATCAGTAATGGGCTTGATTCCTTATGAATCATACATTTTCTAA
+>wzx_145_E68_O141ab/O141ac
+ATGTCGAAATTAAAAAGCAATTTAGTGTATTTAACATTTGCTCAAGCCATAAGCTATATATTTCCTCTTCTGACATTGCCTTACTTAAGTCACAAACTTGATCCTAGTGATTTTGGAATGTTAGGGGTGTGTCAAGCAATAGTTCAATATTTTATAATTGTAACCGATTACGGCTTTAATATTACAACAACAAAAGAAATATCAATAAATCGAAATAATAAAAAAAAGATTTCAAAGATATTTTCCACAACATTATTAGCAAAGATTTTTTTGTTGTTTGTCTCTGCAATAGGGTTAATTATTTCTGGATGGGCTGTGAAGTCGATCTCTGGTTATGAGTTATTATTGATTTGCTGTTTTGTAGGCGTTATTGGTAATACGTTTTATCCTTTATGGTTGTTTCAAGGGACTGAAACCATGAAAATACCTGTAATAATGTCCTCTGGTGCTAAGTTACTTTTACTATTAAGTATTTTTATTTTTGTAAAAGACCGAGCAGATCTCAATATTGCAGCATTATTATTAAATTCAGGAAATTTTTTTGCAGGCATATTGGGATTAATTTACATTAAAACAAGGAAGCTGGTTTTTTGGTATAGGCCAACATTACAAGAAGTCTATATTGTTTTACTTGAAGGCTGGCCAGTATTTATCTCCACTGTTGCAATTAGTTTTTATACTACATTTAACACAGTACTGTTAAGTTATAAAGTCAGTTCTGCAGAAGTAGGCTTTTATAATGCTGCGGATAAAATAAGAATAGCTATACAGTCAATGTTTGGTCCCATTACTCAAGCATTTTATCCTAGAATCGTACATTTATATAAAGTTGAACGAGAAGCTGCTATAAACTTGTTGAACAAAGGCATGCTGTTAATCTTGGGGTTGACGATTCCTTCAGCGTTACTCTTCTTTAATTGTTCAGATTATATAGTAGCACATTATTTGAGTAGTTCCTTTTCTCAGACTGCTTCTTACTTGAAGCTTTTGAGTTTTTTACCAATAATTATTGGTATAGCGACAGTATATTGTAATTGGGGATTACTAGGGGATGGTTATGGAAAAGTAGTTAGTAAGATTTATGTTTCATTTGGCCTAATACACTTTCTGTATGCAACACCACTTATAATAATATTTAAAGTCAATGGACTTATTTTGTCAGTATATATAACACAAACACTGATAACTTTAACTACAATATATCATTACTATAGAAAGGTATATAATGGATTTAATAAATAG
+>wzy_165_CAPL01000042_O5
+TCACTCTGGTACTGCATGTTTTCTTCTCCTGTCAAGAACTGATAATATCAAAAAAATAATAAAAACTAAAATCAGTTGTGTATTAAACAGCATTGAATTAAAACTACTTAGTACAGTTGTTACGGACACAACGTAAAAACTATAAAAACTCATTGTTAACACAGTTTTTTCTCTTGCTCTAAAGTAGATGCATAACAAACCATTTACTATTCCACCGTACATACTGCCAAGCACAATCCCAATGTAACCGAAATTAGAGAAAGTCTCATGTGCAAAAAAACCATTTACATTCCAACCACCATTCTCCGCCATACCTGGCAAATACTGGTACATGAATATCTCTGAAGCCCTTGCTGTTGGAGTAATACTAAGTATTTTGTTAAAAATAGTATCCATGCTAGATAAACCCAGCAAGTTATGTGTAGAAAAGTAATCTGCCGCATAAAATACTGCGGCCTCTTGGGCTATAAACAACCTTTCGACAAGAATATAAAGAAGATAGTCAGAATTATCAAACTGGAATAGAACAACATACATTATCAGTATCAAGGAGAATATTAAAAACGCGGAAAACACATAAATCTTTTTAGTAATTTCCCTCACAGATGAATATGAAACTAAAAGCCCTAAAAAATAAAAAACCAAAGGTGCTTTTTCCCCGTTTATAGCCAATGTTAAAGTTGAAATACAAGTAATAAAAATAAAAAGTAGAAAATGTTTTTTAAATTTTAAATATGATATAAAACAATAATATGAAAGAATTATAGGTATAATACCTGCTAATGTTTTGAAATACCCAATTCCTGAATAATTCTTTGTCACTTCTAATCGTCGGACAGCTATTTCATCCGCAGAAGCTCCCTGTAAAGCCATAGACAATGGCGCAGGATAAATTGATACTATGTAATAAAAAACCAATGCGCATGATAATATACAGAGTGTTAATACTACCTTGTAACTACTCATAATTATAGGACGCGAGTAATAATTATTCCAGTGTATCATTACGGAAGATTGCCCTGAGTATAATGAGCAAAAAACTTCAACAATAAAAGCAGACAGAAAGAATATAAAGAAAGAAATAGTAGTAATAAATAAGCCAAGGTTTTTTACCTCAGCATTATTTGCAATTGGTCCTACAAAAAACGAATCATCCATGACACCTGAATTTATTATAAATGATCCAATAACACAAAATAGCAGCATGGACCAGTAAAGAACGCAATAATAGTTGAGCCTTTTAAAACGAAACACACCCAAGTAATACCCAGGAATAAAACTCAATATTATTATAATAAAATTTAAAGTAAACTCCAT
+>wzy_175_GU014554_O25
+ATGAGCATAAGAATAGAAGAACCAAATAGCACAAAAAGAATTATATTTTTATTTTTACTTTTCCTTGTTTTTCCTGATTTTTTGTTTTATACATTAGGGATTGATAATTTTAGCATTTCAACGATAATCTCCATTATATTGCTTTTTGTTTTTTTAAGGGCTAAAAACACTTGCAAAGATAATTTGCTAATAATAGTAGTATTATTCATATTGTTGTGTTTTAACTGTCTGTTAAGTATGCTATTTAATATTGAACAGGTTTTATCATTTAAAATTGTACTTTCAATGTATAGCATCTTAATAATGGCATACGTCTCCTCTTGTTATGCACAGACTTTGTGGTTATGTTCTGAAGAAATACTTAAGAGATCCGTCTTTTATTTGTTCGCATTTCTTTGCCTTATTGGCATTATAAGTATTCTTTTACAGAAAACTGAGATTATACATGATAAAAGTATGATTCTTTTTCCTGAACCATCAGCATTTGCATTGGTTTTCATACCTATCTTTTCATTTTGTTTATACTATACAAGGGGGGGGGGGGTACTATTGCTCTATATATTATCTTTGGGTATTGCGTTAGGTATCCAGAACTTAACGATGTTAGTAGGCATTGTGATTAGTGTTTTTGTGATGAAAAAAATAACAATAAGGCAAACTATTGTTATATTTTTAGGGGCATGGATTTTTTCCATGATATTAAGTGATTTAGACATTTCTTACTATACATCGCGGCTTGATTTTAAAAATACTACGAACTTATCAGTGCTTGTATATCTTTCAGGAATTGAAAGAGCTTTCTTGAATTTTATTACAAGTTATGGTCTTGGTATTGGTTTTCAACAAATGGGCGTGAATGGGGAGGTAGGAGTGTATCAACAAATTTTAGCTGATCTTGATGCCCCTATGTTAAATATATACGATGGCTCATTTATTTCTTCGAAGTTAATATCTGAGTTTGGGTTTATTGGTGCAATAATGTGCATTTTCTATCTTTTTATTTTTTTCGATTTTATCTGCGTTTCAAAAAAAATAAGAGATATCCACCGCAGTATATTTTAG
\ No newline at end of file

data/O_type.nhr

diff -r 000000000000 -r 8be2feb96994 data/O_type.nhr

data/O_type.nhr

Binary file data/O_type.nhr has changed

data/O_type.nin

diff -r 000000000000 -r 8be2feb96994 data/O_type.nin

data/O_type.nin

Binary file data/O_type.nin has changed

data/O_type.nsq

diff -r 000000000000 -r 8be2feb96994 data/O_type.nsq

data/O_type.nsq

Binary file data/O_type.nsq has changed

data/O_typeDB

diff -r 000000000000 -r 8be2feb96994 data/O_typeDB

data/O_typeDB

Binary file data/O_typeDB has changed

data/O_typeDB

diff -r 000000000000 -r 8be2feb96994 data/O_typeDB.dbtype

data/O_typeDB

Binary file data/O_typeDB.dbtype has changed

data/O_typeDB

diff -r 000000000000 -r 8be2feb96994 data/O_typeDB.index

data/O_typeDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/O_typeDB.index Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,480 @@
+0 0 1229
+1 1229 1460
+2 2689 1517
+3 4206 1220
+4 5426 1316
+5 6742 1409
+6 8151 1238
+7 9389 1238
+8 10627 1274
+9 11901 1088
+10 12989 956
+11 13945 980
+12 14925 1187
+13 16112 1022
+14 17134 1298
+15 18432 1496
+16 19928 1247
+17 21175 1253
+18 22428 1205
+19 23633 1244
+20 24877 1241
+21 26118 1244
+22 27362 1028
+23 28390 1145
+24 29535 1190
+25 30725 1208
+26 31933 1007
+27 32940 1187
+28 34127 1022
+29 35149 1211
+30 36360 1241
+31 37601 1259
+32 38860 1277
+33 40137 1367
+34 41504 1208
+35 42712 1268
+36 43980 1448
+37 45428 1055
+38 46483 1283
+39 47766 1334
+40 49100 1154
+41 50254 1088
+42 51342 1151
+43 52493 1046
+44 53539 755
+45 54294 1259
+46 55553 1208
+47 56761 1220
+48 57981 1253
+49 59234 1247
+50 60481 1463
+51 61944 1403
+52 63347 1064
+53 64411 1055
+54 65466 1070
+55 66536 1016
+56 67552 1190
+57 68742 1151
+58 69893 1046
+59 70939 752
+60 71691 1259
+61 72950 1247
+62 74197 1262
+63 75459 1394
+64 76853 1520
+65 78373 1262
+66 79635 1280
+67 80915 1235
+68 82150 1292
+69 83442 1163
+70 84605 1103
+71 85708 1319
+72 87027 1151
+73 88178 1049
+74 89227 734
+75 89961 1241
+76 91202 1235
+77 92437 1535
+78 93972 1424
+79 95396 1541
+80 96937 1274
+81 98211 1280
+82 99491 1244
+83 100735 1178
+84 101913 1103
+85 103016 1190
+86 104206 1346
+87 105552 1151
+88 106703 1253
+89 107956 755
+90 108711 1259
+91 109970 1310
+92 111280 1241
+93 112521 1424
+94 113945 1235
+95 115180 1346
+96 116526 1280
+97 117806 1382
+98 119188 1076
+99 120264 1205
+100 121469 1238
+101 122707 1346
+102 124053 1151
+103 125204 1151
+104 126355 755
+105 127110 1433
+106 128543 1481
+107 130024 1418
+108 131442 1256
+109 132698 1193
+110 133891 1415
+111 135306 1274
+112 136580 1166
+113 137746 1235
+114 138981 1262
+115 140243 1340
+116 141583 1346
+117 142929 1151
+118 144080 1250
+119 145330 728
+120 146058 1427
+121 147485 1283
+122 148768 1163
+123 149931 1490
+124 151421 1193
+125 152614 1256
+126 153870 1268
+127 155138 1229
+128 156367 1124
+129 157491 1253
+130 158744 1076
+131 159820 1154
+132 160974 1151
+133 162125 1055
+134 163180 743
+135 163923 1433
+136 165356 1322
+137 166678 1223
+138 167901 1430
+139 169331 1187
+140 170518 1436
+141 171954 1232
+142 173186 1214
+143 174400 1094
+144 175494 1106
+145 176600 1253
+146 177853 1178
+147 179031 1193
+148 180224 1334
+149 181558 755
+150 182313 1190
+151 183503 1316
+152 184819 1304
+153 186123 1220
+154 187343 1505
+155 188848 1268
+156 190116 1253
+157 191369 1205
+158 192574 1229
+159 193803 1106
+160 194909 1235
+161 196144 728
+162 196872 1193
+163 198065 797
+164 198862 797
+165 199659 1523
+166 201182 1262
+167 202444 1232
+168 203676 1223
+169 204899 1214
+170 206113 1562
+171 207675 1466
+172 209141 1025
+173 210166 1232
+174 211398 1325
+175 212723 1055
+176 213778 1244
+177 215022 1193
+178 216215 788
+179 217003 788
+180 217791 1238
+181 219029 1262
+182 220291 1445
+183 221736 1490
+184 223226 1181
+185 224407 1397
+186 225804 1259
+187 227063 1025
+188 228088 1085
+189 229173 1046
+190 230219 1175
+191 231394 1046
+192 232440 1190
+193 233630 788
+194 234418 788
+195 235206 1262
+196 236468 1265
+197 237733 1397
+198 239130 1484
+199 240614 1295
+200 241909 1268
+201 243177 1274
+202 244451 1259
+203 245710 1238
+204 246948 1118
+205 248066 1154
+206 249220 1313
+207 250533 1193
+208 251726 776
+209 252502 776
+210 253278 1259
+211 254537 1133
+212 255670 1223
+213 256893 1448
+214 258341 1289
+215 259630 1268
+216 260898 1250
+217 262148 1136
+218 263284 1154
+219 264438 1307
+220 265745 1178
+221 266923 1133
+222 268056 1190
+223 269246 797
+224 270043 797
+225 270840 1247
+226 272087 1226
+227 273313 1205
+228 274518 1448
+229 275966 1142
+230 277108 1394
+231 278502 1445
+232 279947 1229
+233 281176 1121
+234 282297 1202
+235 283499 1082
+236 284581 1133
+237 285714 1190
+238 286904 782
+239 287686 782
+240 288468 1250
+241 2897..292428 1517
+244 293945 1256
+245 295201 1394
+246 296595 1259
+247 297854 1250
+248 299104 1403
+249 300507 1160
+250 301667 1142
+251 302809 1325
+252 304134 1055
+253 305189 842
+254 306031 842
+255 306873 1238
+256 308111 1265
+257 309376 1205
+258 310581 1274
+259 311855 1382
+260 313237 1394
+261 314631 1238
+262 315869 1208
+263 317077 1157
+264 318234 1235
+265 319469 1133
+266 320602 1325
+267 321927 965
+268 322892 788
+269 323680 788
+270 324468 1250
+271 325718 1232
+272 326950 1154
+273 328104 1487
+274 329591 1250
+275 330841 1289
+276 332130 1106
+277 333236 1199
+278 334435 1277
+279 335712 1214
+280 336926 1334
+281 338260 1046
+282 339306 1148
+283 340454 797
+284 341251 797
+285 342048 1259
+286 343307 1253
+287 344560 1460
+288 346020 1487
+289 347507 1244
+290 348751 1358
+291 350109 1151
+292 351260 1214
+293 352474 1160
+294 353634 1241
+295 354875 1289
+296 356164 1046
+297 357210 1142
+298 358352 782
+299 359134 782
+300 359916 1412
+301 361328 1280
+302 362608 1274
+303 363882 1274
+304 365156 1256
+305 366412 1394
+306 367806 1181
+307 368987 1142
+308 370129 1214
+309 371343 1193
+310 372536 1106
+311 373642 1169
+312 374811 1109
+313 375920 803
+314 376723 803
+315 377526 1238
+316 378764 1280
+317 380044 1268
+318 381312 1274
+319 382586 1457
+320 384043 1394
+321 385437 1169
+322 386606 1124
+323 387730 1514
+324 389244 1109
+325 390353 1334
+326 391687 1169
+327 392856 965
+328 393821 821
+329 394642 821
+330 395463 1220
+331 396683 1280
+332 397963 1202
+333 399165 1445
+334 400610 1253
+335 401863 1241
+336 403104 1334
+337 404438 1157
+338 405595 1253
+339 406848 1184
+340 408032 1229
+341 409261 1151
+342 410412 1334
+343 411746 782
+344 412528 782
+345 413310 1196
+346 414506 1202
+347 415708 1250
+348 416958 1259
+349 418217 1256
+350 419473 1241
+351 420714 1334
+352 422048 965
+353 423013 1157
+354 424170 1085
+355 425255 1346
+356 426601 1145
+357 427746 1100
+358 428846 743
+359 429589 743
+360 430332 1208
+361 431540 1286
+362 432826 1304
+363 434130 1277
+364 435407 1268
+365 436675 1268
+366 437943 1334
+367 439277 1040
+368 440317 1172
+369 441489 1211
+370 442700 1373
+371 444073 1103
+372 445176 1160
+373 446336 770
+374 447106 1274
+375 448380 1262
+376 449642 1190
+377 450832 1244
+378 452076 1271
+379 453347 1274
+380 454621 1268
+381 455889 1193
+382 457082 1295
+383 458377 1115
+384 459492 1181
+385 460673 1280
+386 461953 1253
+387 463206 1253
+388 464459 782
+389 465241 1250
+390 466491 1289
+391 467780 1229
+392 469009 1298
+393 470307 1286
+394 471593 1286
+395 472879 1265
+396 474144 1148
+397 475292 1061
+398 476353 1031
+399 477384 1190
+400 478574 689
+401 479263 1025
+402 480288 971
+403 481259 1217
+404 482476 1445
+405 483921 1262
+406 485183 1265
+407 486448 1280
+408 487728 1259
+409 488987 1250
+410 490237 1268
+411 491505 1127
+412 492632 1052
+413 493684 1325
+414 495009 1067
+415 496076 1094
+416 497170 1169
+417 498339 1325
+418 499664 1298
+419 500962 1325
+420 502287 1232
+421 503519 1265
+422 504784 1280
+423 506064 1241
+424 507305 1268
+425 508573 1274
+426 509847 1325
+427 511172 1334
+428 512506 1241
+429 513747 1100
+430 514847 1151
+431 515998 1187
+432 517185 1046
+433 518231 1298
+434 519529 1046
+435 520575 1073
+436 521648 1286
+437 522934 1193
+438 524127 1385
+439 525512 1304
+440 526816 1448
+441 528264 1229
+442 529493 1172
+443 530665 1223
+444 531888 1076
+445 532964 1151
+446 534115 1169
+447 535284 1115
+448 536399 977
+449 537376 1244
+450 538620 1403
+451 540023 1253
+452 541276 1430
+453 542706 1280
+454 543986 1202
+455 545188 1304
+456 546492 1085
+457 547577 1160
+458 548737 1208
+459 549945 1169
+460 551114 1151
+461 552265 1187
+462 553452 1115
+463 554567 1304
+464 555871 1319
+465 557190 1208
+466 558398 1340
+467 559738 1238
+468 560976 1223
+469 562199 1274
+470 563473 1214
+471 564687 1238
+472 565925 1232
+473 567157 1181
+474 568338 1043
+475 569381 980
+476 570361 1187
+477 571548 1265
+478 572813 1217
+479 574030 1064

data/O_typeDB

diff -r 000000000000 -r 8be2feb96994 data/O_typeDB.lookup

data/O_typeDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/O_typeDB.lookup Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,480 @@
+0 wzx_1_GU299791_O1 0
+1 wzx_39_EU296410_O32 0
+2 wzx_74_AB812028_O69 0
+3 wzx_109_EU694095_O107 0
+4 wzx_144_AB812060_O140 0
+5 wzx_179_AB812073_O175 0
+6 wzx_214_AB811620_O44 0
+7 wzy_16_DQ851855_O22 0
+8 wzy_58_AB812026_O65 0
+9 wzy_91_EU296405_O112ac 0
+10 wzy_123_AY657020_O155 0
+11 wzy_159_AB353132_O55 0
+12 wzy_198_AF061251_O157 0
+13 wzy_409_KY115223_O1 0
+14 wzt_7_D43637_O9 0
+15 wzx_5_EU694097_O3 0
+16 wzx_40_AB811611_O33 0
+17 wzx_75_FN995094_O70 0
+18 wzx_110_AB812048_O108 0
+19 wzx_145_DQ868765_O141 0
+20 wzx_180_AB812074_O176 0
+21 wzx_215_AB812057_O133 0
+22 wzy_17_AB811607_O23 0
+23 wzy_60_AB812028_O69 0
+24 wzy_92_AF172324_O113 0
+25 wzy_124_AB812065_O156 0
+26 wzy_160_GU299791_O1 0
+27 wzy_201_JH953200_O157 0
+28 wzy_410_KY115225_O1 0
+29 wzt_8_AB812022_O60 0
+30 wzx_7_AY568960_O4 0
+31 wzx_41_AB811612_O34 0
+32 wzx_76_GU445927_O71 0
+33 wzx_111_HM485572_O109 0
+34 wzx_146_EU294164_O143 0
+35 wzx_181_DQ008593_O177 0
+36 wzx_216_KP710595_O186 0
+37 wzy_18_DQ220292_O24 0
+38 wzy_61_FN995094_O70 0
+39 wzy_93_AY573377_O114 0
+40 wzy_125_GU068044_O158 0
+41 wzy_162_EU694097_O3 0
+42 wzy_202_EF027120_O103 0
+43 wzy_411_KY115226_O1 0
+44 wzt_9_AB812038_O89 0
+45 wzx_8_AB811596_O5 0
+46 wzx_42_FJ940774_O35 0
+47 wzx_77_DQ000313_O73 0
+48 wzx_112_AB812049_O110 0
+49 wzx_147_AB812061_O142 0
+50 wzx_182_AB812076_O179 0
+51 wzx_217_SAMEA7184437_O188 0
+52 wzy_19_GU014554_O25 0
+53 wzy_62_JN887675_O111 0
+54 wzy_94_GU068041_O115 0
+55 wzy_126_EU294176_O159 0
+56 wzy_163_AY568960_O4 0
+57 wzy_203_EF027119_O103 0
+58 wzy_412_KY115229_O2 0
+59 wzt_10_AB812040_O92 0
+60 wzx_9_AJ426045_O6 0
+61 wzx_43_AB811613_O36 0
+62 wzx_78_AB812030_O74 0
+63 wzx_113_EU296413_O112ab 0
+64 wzx_149_AB812062_O144 0
+65 wzx_183_JQ751058_O180 0
+66 wzx_218_KY115223_O1 0
+67 wzy_20_GU014555_O27 0
+68 wzy_63_GU445927_O71 0
+69 wzy_95_AB812051_O116 0
+70 wzy_127_AB812066_O160 0
+71 wzy_164_AB811596_O5 0
+72 wzy_204_EF027116_O103 0
+73 wzy_413_KY115228_O2 0
+74 wzt_11_AB812042_O95 0
+75 wzx_10_CP002185_O6 0
+76 wzx_44_AB811614_O37 0
+77 wzx_79_GU299795_O75 0
+78 wzx_114_EU296405_O112ac 0
+79 wzx_150_DQ465249_O146 0
+80 wzx_184_AB812078_O181 0
+81 wzx_219_KY115225_O1 0
+82 wzy_21_AB811608_O28ab 0
+83 wzy_64_AB812030_O74 0
+84 wzy_96_HM204927_O118 0
+85 wzy_128_GU220361_O161 0
+86 wzy_166_AJ426423_O6 0
+87 wzy_205_AP010958_O103 0
+88 wzy_416_AB972419_O123 0
+89 wzt_12_CP011061_O101 0
+90 wzx_12_AB811597_O6 0
+91 wzx_45_AB811615_O38 0
+92 wzx_80_AB812031_O76 0
+93 wzx_115_AF172324_O113 0
+94 wzx_151_DQ868766_O147 0
+95 wzx_185_AB812079_O182 0
+96 wzx_220_KY115226_O1 0
+97 wzy_22_DQ462205-FJ539194_O28ac/O42 0
+98 wzy_65_GU299795_O75 0
+99 wzy_97_GQ499368_O119 0
+100 wzy_129_AB812068_O163 0
+101 wzy_167_AJ426045_O6 0
+102 wzy_206_EF027115_O103 0
+103 wzy_417_AB972421_O13/O129/O135 0
+104 wzt_13_AB812067_O162 0
+105 wzx_14_CP003034_O7 0
+106 wzx_46_AB811616_O39 0
+107 wzx_81_FJ940775_O78 0
+108 wzx_116_AY573377_O114 0
+109 wzx_152_DQ167407_O148 0
+110 wzx_186_AB627352_O183 0
+111 wzx_221_KY115229_O2 0
+112 wzy_23_EU294173_O29 0
+113 wzy_66_AB812031_O76 0
+114 wzy_98_AB812052_O120 0
+115 wzy_130_GU068045_O165 0
+116 wzy_168_CP002185_O6 0
+117 wzy_207_EF027106_O103 0
+118 wzy_420_NJRR01_O57 0
+119 wzt_14_AB812044_O97 0
+120 wzx_15_AB490074_O7 0
+121 wzx_47_EU296417_O40 0
+122 wzx_82_EU294162_O79 0
+123 wzx_117_GU068041_O115 0
+124 wzx_153_AAJT02000037_O148 0
+125 wzx_187_AB812080_O184 0
+126 wzx_222_KY115228_O2 0
+127 wzy_24_AB811610_O30 0
+128 wzy_67_FJ940775_O78 0
+129 wzy_99_DQ676934-AB812082_O123/O186 0
+130 wzy_131_GU299794_O166 0
+131 wzy_169_AF125322_O7 0
+132 wzy_208_EF027117_O103 0
+133 wzy_232_AB627352_O183 0
+134 wzt_15_KY379508_O62 0
+135 wzx_16_AF125322_O7 0
+136 wzx_48_AB811617_O41 0
+137 wzx_83_AB812032_O80 0
+138 wzx_119_AB812051_O116 0
+139 wzx_155_DQ091854_O149 0
+140 wzx_188_AB812081_O185 0
+141 wzx_223_KJ778799_O178 ..0 wzy_146_AB812079_O182 0
+341 wzy_186_EU296424_O129 0
+342 wzy_224_AB972416_O77 0
+343 wzm_13_AB812067_O162 0
+344 wzm_13_AB812067_O162 0
+345 wzx_30_DQ220292_O24 0
+346 wzx_63_DQ220293_O56 0
+347 wzx_98_AB812043_O96 0
+348 wzx_135_EU296424_O129 0
+349 wzx_170_GU299794_O166 0
+350 wzx_204_JN850039_O145 0
+351 wzy_7_DQ000313_O73 0
+352 wzy_48_EU549863_O2 0
+353 wzy_82_DQ180602_O98 0
+354 wzy_114_EU294164_O143 0
+355 wzy_147_AB812080_O184 0
+356 wzy_187_DQ167407_O148 0
+357 wzy_225_KJ778799_O178 0
+358 wzm_14_AB812044_O97 0
+359 wzm_14_AB812044_O97 0
+360 wzx_31_AB811607_O23 0
+361 wzx_64_AY654590_O59 0
+362 wzx_99_DQ180602_O98 0
+363 wzx_136_EU296421_O130 0
+364 wzx_171_EU296408_O167 0
+365 wzx_206_JN887675_O111 0
+366 wzy_8_DQ000315_O106 0
+367 wzy_49_AB812020_O51 0
+368 wzy_83_AB812045_O100 0
+369 wzy_115_AB812062_O144 0
+370 wzy_148_AB812081_O185 0
+371 wzy_189_HM204926_O151 0
+372 wzy_226_SAMEA7184437_O188 0
+373 wzm_15_KY379508_O62 0
+374 wzx_400_KP835694_O125ab 0
+375 wzx_32_GU014554_O25 0
+376 wzx_64_EU294175_O58 0
+377 wzx_100_AB812045_O100 0
+378 wzx_137_AB812055_O131 0
+379 wzx_172_EU296403_O168 0
+380 wzx_207_AP010960_O111 0
+381 wzy_9_GU299793_O18 0
+382 wzy_50_EU289392_O53 0
+383 wzy_84_AF361371_O104 0
+384 wzy_116_DQ465249_O146 0
+385 wzy_149_AB812083_O187 0
+386 wzy_190_AB812078_O181 0
+387 wzy_227_AB812082_O186 0
+388 wzm_16_AB812046_O101 0
+389 wzx_401_AB811602_O18ab 0
+390 wzx_33_GU014555_O27 0
+391 wzx_66_GU220362_O61 0
+392 wzx_102_AF361371_O104 0
+393 wzx_138_AB812056_O132 0
+394 wzx_173_AB812069_O169 0
+395 wzx_208_AF529080_O26 0
+396 wzy_10_AB811602_O18ab 0
+397 wzy_51_AB812085_O54 0
+398 wzy_85_EU294171_O105 0
+399 wzy_117_DQ868766_O147 0
+400 wzy_152_AIGX01000028_O45 0
+401 wzy_192_AF529080_O26 0
+402 wzy_228_KP710595_O186 0
+403 wzt_1_AB010150_O8 0
+404 wzx_405_5564-64_O128ac 0
+405 wzx_34_AB811608_O28ab 0
+406 wzx_68_EU549862_O63 0
+407 wzx_103_KB021482_O104 0
+408 wzx_139_EU296423_O135 0
+409 wzx_174_AB812070_O170 0
+410 wzx_209_EF027106_O103 0
+411 wzy_11_AB811604_O19 0
+412 wzy_52_DQ220293_O56 0
+413 wzy_86_EU694095_O107 0
+414 wzy_118_DQ868764_O149 0
+415 wzy_153_CU463050_O45 0
+416 wzy_193_JH964427_O157 0
+417 wzy_400_SAMEA3529396_O125ab 0
+418 wzt_2_AB010294_O9 0
+419 wzy_400_KP835694_O125ab 0
+420 wzx_35_AB811609_O28ac 0
+421 wzx_69_FJ539195_O63 0
+422 wzx_104_CP003301_O104 0
+423 wzx_140_AB812059_O136 0
+424 wzx_175_AB812071_O171 0
+425 wzx_210_AB812054_O127 0
+426 wzy_12_KJ778793_O20 0
+427 wzy_53_EU294175_O58 0
+428 wzy_87_AB812048_O108 0
+429 wzy_119_EU294168_O150 0
+430 wzy_154_JN859208_O45 0
+431 wzy_194_AB602249_O157 0
+432 wzy_405_SAMEA3529399_O128ac 0
+433 wzt_3_AB010293_O9a 0
+434 wzy_405_5564-64_O128ac 0
+435 wzx_36_DQ462205-FJ539194_O28ac/O42 0
+436 wzx_70_AB812025_O64 0
+437 wzx_105_AFPS01000083_O104 0
+438 wzx_141_GU068043_O137 0
+439 wzx_176_AY545992_O172 0
+440 wzx_211_AB812082_O186 0
+441 wzy_13_GU068043_O137 0
+442 wzy_54_AY654590_O59 0
+443 wzy_88_HM485572_O109 0
+444 wzy_120_EU294170_O152 0
+445 wzy_156_JN859205_O45 0
+446 wzy_195_JH970567_O157 0
+447 wzy_406_SAMEA3529400_O141ab 0
+448 wzt_4_AY528413_O52 0
+449 wzx_145_E68_O141ab/O141ac 0
+450 wzx_37_EU294173_O29 0
+451 wzx_71_AB812026_O65 0
+452 wzx_107_EU294171_O105 0
+453 wzx_142_DQ109551_O138 0
+454 wzx_177_GU068046_O173 0
+455 wzx_212_AB812058_O134 0
+456 wzy_14_EU694098_O21 0
+457 wzy_55_GU220362_O61 0
+458 wzy_89_AB812049_O110 0
+459 wzy_121_KJ755551_O153 0
+460 wzy_157_AY771223_O45 0
+461 wzy_196_AB602253_O157 0
+462 wzy_407_SAMEA3529401_O141ac 0
+463 wzt_5_FJ940773_O99 0
+464 wzy_165_CAPL01000042_O5 0
+465 wzx_38_AB811610_O30 0
+466 wzx_72_DQ069297_O66 0
+467 wzx_108_DQ000315_O106 0
+468 wzx_143_DQ109552_O139 0
+469 wzx_178_DQ008592_O174 0
+470 wzx_213_AB812027_O68 0
+471 wzy_15_AB811606_O22 0
+472 wzy_57_AB812025_O64 0
+473 wzy_90_EU296413_O112ab 0
+474 wzy_122_AB812064_O154 0
+475 wzy_158_CP003109_O55 0
+476 wzy_197_AB602250_O157 0
+477 wzy_408_DQ069297_O66 0
+478 wzt_6_AB811598_O8 0
+479 wzy_175_GU014554_O25 0

data/O_typeDB

diff -r 000000000000 -r 8be2feb96994 data/O_typeDB.source

data/O_typeDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/O_typeDB.source Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,1 @@
+0 O_type.fsa

data/O_typeDB

diff -r 000000000000 -r 8be2feb96994 data/O_typeDB_h

data/O_typeDB

Binary file data/O_typeDB_h has changed

data/O_typeDB

diff -r 000000000000 -r 8be2feb96994 data/O_typeDB_h.dbtype

data/O_typeDB

Binary file data/O_typeDB_h.dbtype has changed

data/O_typeDB

diff -r 000000000000 -r 8be2feb96994 data/O_typeDB_h.index

data/O_typeDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/O_typeDB_h.index Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,480 @@
+0 0 19
+1 19 21
+2 40 21
+3 61 23
+4 84 23
+5 107 23
+6 130 22
+7 152 21
+8 173 21
+9 194 24
+10 218 23
+11 241 22
+12 263 23
+13 286 21
+14 307 17
+15 324 19
+16 343 21
+17 364 21
+18 385 23
+19 408 23
+20 431 23
+21 454 23
+22 477 21
+23 498 21
+24 519 22
+25 541 23
+26 564 21
+27 585 23
+28 608 21
+29 629 20
+30 649 19
+31 668 21
+32 689 21
+33 710 23
+34 733 23
+35 756 23
+36 779 23
+37 802 21
+38 823 21
+39 844 22
+40 866 23
+41 889 21
+42 910 23
+43 933 21
+44 954 20
+45 974 19
+46 993 21
+47 1014 21
+48 1035 23
+49 1058 23
+50 1081 23
+51 1104 27
+52 1131 21
+53 1152 22
+54 1174 22
+55 1196 23
+56 1219 21
+57 1240 23
+58 1263 21
+59 1284 21
+60 1305 19
+61 1324 21
+62 1345 21
+63 1366 25
+64 1391 23
+65 1414 23
+66 1437 21
+67 1458 21
+68 1479 21
+69 1500 22
+70 1522 23
+71 1545 21
+72 1566 23
+73 1589 21
+74 1610 21
+75 1631 20
+76 1651 21
+77 1672 21
+78 1693 25
+79 1718 23
+80 1741 23
+81 1764 21
+82 1785 23
+83 1808 21
+84 1829 22
+85 1851 23
+86 1874 21
+87 1895 23
+88 1918 23
+89 1941 22
+90 1963 20
+91 1983 21
+92 2004 21
+93 2025 23
+94 2048 23
+95 2071 23
+96 2094 21
+97 2115 36
+98 2151 21
+99 2172 22
+100 2194 23
+101 2217 21
+102 2238 23
+103 2261 32
+104 2293 22
+105 2315 20
+106 2335 21
+107 2356 21
+108 2377 23
+109 2400 23
+110 2423 23
+111 2446 21
+112 2467 21
+113 2488 21
+114 2509 22
+115 2531 23
+116 2554 21
+117 2575 23
+118 2598 20
+119 2618 21
+120 2639 20
+121 2659 21
+122 2680 21
+123 2701 23
+124 2724 27
+125 2751 23
+126 2774 21
+127 2795 21
+128 2816 21
+129 2837 36
+130 2873 23
+131 2896 21
+132 2917 23
+133 2940 23
+134 2963 21
+135 2984 20
+136 3004 21
+137 3025 21
+138 3046 23
+139 3069 23
+140 3092 23
+141 3115 23
+142 3138 21
+143 3159 21
+144 3180 23
+145 3203 23
+146 3226 21
+147 3247 23
+148 3270 35
+149 3305 22
+150 3327 20
+151 3347 21
+152 3368 21
+153 3389 23
+154 3412 23
+155 3435 23
+156 3458 23
+157 3481 21
+158 3502 21
+159 3523 23
+160 3546 23
+161 3569 21
+162 3590 23
+163 3613 19
+164 3632 19
+165 3651 21
+166 3672 21
+167 3693 21
+168 3714 37
+169 3751 23
+170 3774 22
+171 3796 23
+172 3819 21
+173 3840 21
+174 3861 25
+175 3886 23
+176 3909 21
+177 3930 23
+178 3953 19
+179 3972 19
+180 3991 21
+181 4012 21
+182 4033 21
+183 4054 23
+184 4077 23
+185 4100 23
+186 4123 27
+187 4150 21
+188 4171 21
+189 4192 25
+190 4217 23
+191 4240 22
+192 4262 23
+193 4285 20
+194 4305 19
+195 4324 21
+196 4345 21
+197 4366 21
+198 4387 23
+199 4410 23
+200 4433 24
+201 4457 29
+202 4486 21
+203 4507 21
+204 4528 23
+205 4551 23
+206 4574 22
+207 4596 23
+208 4619 20
+209 4639 20
+210 4659 26
+211 4685 21
+212 4706 21
+213 4727 23
+214 4750 23
+215 4773 23
+216 4796 25
+217 4821 21
+218 4842 21
+219 4863 23
+220 4886 23
+221 4909 23
+222 4932 23
+223 4955 20
+224 4975 20
+225 4995 21
+226 5016 21
+227 5037 21
+228 5058 23
+229 5081 23
+230 5104 23
+231 5127 29
+232 5156 21
+233 5177 21
+234 5198 23
+235 5221 23
+236 5244 23
+237 5267 23
+238 5290 21
+239 5311 21
+240 5332 21
+241 5353 21
+242 5374 21
+243 5395 23
+244 5418 23
+245 5441 23
+246 5464 20
+247 5484 21
+248 5505 21
+249 5526 23
+250 5549 23
+251 5572 23
+252 5595 24
+253 5619 19
+254 5638 19
+255 5657 34
+256 5691 30
+257 5721 21
+258 5742 25
+259 5767 23
+260 5790 23
+261 5813 20
+262 5833 21
+263 5854 21
+264 5875 23
+265 5898 23
+266 5921 23
+267 5944 22
+268 5966 17
+269 5983 17
+270 6000 23
+271 6023 21
+272 6044 21
+273 6065 23
+274 6088 23
+275 6111 27
+276 6138 20
+277 6158 21
+278 6179 21
+279 6200 23
+280 6223 23
+281 6246 23
+282 6269 24
+283 6293 20
+284 6313 20
+285 6333 21
+286 6354 21
+287 6375 21
+288 6396 23
+289 6419 23
+290 6442 27
+291 6469 34
+292 6503 21
+293 6524 21
+294 6545 23
+295 6568 23
+296 6591 23
+297 6614 23
+298 6637 21
+299 6658 21
+300 6679 21
+301 6700 21
+302 6721 21
+303 6742 23
+304 6765 23
+305 6788 23
+306 6811 20
+307 6831 21
+308 6852 21
+309 6873 23
+310 6896 23
+311 6919 23
+312 6942 22
+313 6964 21
+314 6985 21
+315 7006 21
+316 7027 21
+317 7048 21
+318 7069 23
+319 7092 23
+320 7115 23
+321 7138 20
+322 7158 21
+323 7179 21
+324 7200 23
+325 7223 23
+326 7246 23
+327 7269 21
+328 7290 21
+329 7311 21
+330 7332 21
+331 7353 21
+332 7374 21
+333 7395 25
+334 7420 23
+335 7443 23
+336 7466 20
+337 7486 21
+338 7507 21
+339 7528 23
+340 7551 23
+341 7574 23
+342 7597 22
+343 7619 22
+344 7641 22
+345 7663 21
+346 7684 21
+347 7705 21
+348 7726 23
+349 7749 23
+350 7772 23
+351 7795 20
+352 7815 20
+353 7835 21
+354 7856 23
+355 7879 23
+356 7902 23
+357 7925 23
+358 7948 21
+359 7969 21
+360 7990 21
+361 8011 21
+362 8032 21
+363 8053 23
+364 8076 23
+365 8099 23
+366 8122 21
+367 8143 21
+368 8164 22
+369 8186 23
+370 8209 23
+371 8232 23
+372 8255 27
+373 8282 21
+374 8303 25
+375 8328 21
+376 8349 21
+377 8370 23
+378 8393 23
+379 8416 23
+380 8439 23
+381 8462 20
+382 8482 21
+383 8503 22
+384 8525 23
+385 8548 23
+386 8571 23
+387 8594 23
+388 8617 22
+389 8639 24
+390 8663 21
+391 8684 21
+392 8705 23
+393 8728 23
+394 8751 23
+395 8774 22
+396 8796 23
+397 8819 21
+398 8840 22
+399 8862 23
+400 8885 26
+401 8911 22
+402 8933 23
+403 8956 19
+404 8975 24
+405 8999 23
+406 9022 21
+407 9043 23
+408 9066 23
+409 9089 23
+410 9112 23
+411 9135 21
+412 9156 21
+413 9177 22
+414 9199 23
+415 9222 22
+416 9244 23
+417 9267 29
+418 9296 19
+419 9315 25
+420 9340 23
+421 9363 21
+422 9384 23
+423 9407 23
+424 9430 23
+425 9453 23
+426 9476 21
+427 9497 21
+428 9518 22
+429 9540 23
+430 9563 22
+431 9585 23
+432 9608 29
+433 9637 20
+434 9657 24
+435 9681 36
+436 9717 21
+437 9738 27
+438 9765 23
+439 9788 23
+440 9811 23
+441 9834 22
+442 9856 21
+443 9877 22
+444 9899 23
+445 9922 22
+446 9944 23
+447 9967 29
+448 9996 20
+449 10016 27
+450 10043 21
+451 10064 21
+452 10085 23
+453 10108 23
+454 10131 23
+455 10154 23
+456 10177 21
+457 10198 21
+458 10219 22
+459 10241 23
+460 10264 22
+461 10286 23
+462 10309 29
+463 10338 20
+464 10358 25
+465 10383 21
+466 10404 21
+467 10425 23
+468 10448 23
+469 10471 23
+470 10494 22
+471 10516 21
+472 10537 21
+473 10558 24
+474 10582 23
+475 10605 22
+476 10627 23
+477 10650 22
+478 10672 19
+479 10691 22

data/SequenceTyping_db.txt

diff -r 000000000000 -r 8be2feb96994 data/SequenceTyping_db.txt

data/SequenceTyping_db.txt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/SequenceTyping_db.txt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,3 @@
+Enterobase
+Allele database: v20181009
+Sequence database: v20181009

data/SeroTyping_db.txt

diff -r 000000000000 -r 8be2feb96994 data/SeroTyping_db.txt

data/SeroTyping_db.txt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/SeroTyping_db.txt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,3 @@
+Statens Serum Institut & Technical University of Denmark
+O type database: v20200924
+H type database: v20170123

data/ShigatoxinTyping_db.txt

diff -r 000000000000 -r 8be2feb96994 data/ShigatoxinTyping_db.txt

data/ShigatoxinTyping_db.txt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/ShigatoxinTyping_db.txt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,2 @@
+Statens Serum Institut & Technical University of Denmark
+Shigatoxin subtype database: v20180910

data/ViruloTyping_db.txt

diff -r 000000000000 -r 8be2feb96994 data/ViruloTyping_db.txt

data/ViruloTyping_db.txt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/ViruloTyping_db.txt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,2 @@
+Statens Serum Institut & Technical University of Denmark
+Virulotype database: v20200722 (with additions v20201121)

data/amrfinder/AMR.LIB

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR.LIB

data/amrfinder/AMR.LIB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMR.LIB Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,565218 @@
+HMMER3/f [3.1b2 | February 2015]
+NAME 154989_fosA-NCBI
+ACC   NF000026.1
+DESC  NCBI: FosA/FosA2 family fosfomycin resistance glutathione transferase
+LENG  141
+ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Tue Aug 27 12:35:11 2019
+NSEQ  1
+EFFN  0.378906
+CKSUM 1186568173
+GA    275 275
+TC    275 275
+NC    275 275
+STATS LOCAL MSV       -9.7405  0.71056
+STATS LOCAL VITERBI  -10.9503  0.71056
+STATS LOCAL FORWARD   -4.3128  0.71056
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.44139  4.05182  2.90105  2.70994  3.19879  2.83251  3.57619  2.97322  2.84440  2.32940  3.74448  3.21132  3.40506  3.15254  3.05023  2.64128  2.83794  2.66995  4.16255  3.27400
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03461  3.77673  4.49907  0.61958  0.77255  0.00000        *
+      1   2.89749  4.46272  3.94768  3.53638  3.17194  3.76237  4.29385  2.33825  3.30869  1.78359  1.57508  3.82494  4.22470  3.69835  3.52477  3.23543  3.20211  2.33255  4.99846  3.75025      1 m - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03461  3.77673  4.49907  0.61958  0.77255  0.48576  0.95510
+      2   3.05024  4.54260  4.03392  3.67645  3.10418  3.85738  4.36228  2.30688  3.44499  1.00320  3.16272  3.96078  4.31135  3.83644  3.63551  3.42143  3.35009  2.31873  4.94563  3.64590      2 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03461  3.77673  4.49907  0.61958  0.77255  0.48576  0.95510
+      3   2.81043  4.78761  2.84581  2.60235  3.94242  3.30568  3.75867  3.56135  2.43074  3.07300  4.10684  3.05998  3.85986  1.41525  2.71548  2.86378  3.10904  3.29803  5.23325  3.92150      3 q - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03461  3.77673  4.49907  0.61958  0.77255  0.48576  0.95510
+      4   2.27294  4.19044  3.12785  2.94209  3.98201  2.92230  4.05319  3.49296  3.00917  3.22179  4.15813  3.18047  3.65381  3.36680  3.29620  1.24540  2.74641  3.04931  5.36292  4.06569      4 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03461  3.77673  4.49907  0.61958  0.77255  0.48576  0.95510
+      5   3.05024  4.54260  4.03392  3.67645  3.10418  3.85738  4.36228  2.30688  3.44499  1.00320  3.16272  3.96078  4.31135  3.83644  3.63551  3.42143  3.35009  2.31873  4.94563  3.64590      5 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03461  3.77673  4.49907  0.61958  0.77255  0.48576  0.95510
+      6   2.64850  4.63703  2.66442  2.54171  3.98589  3.12309  3.85174  3.67836  2.74894  3.33717  4.29527  1.33997  3.77165  3.12679  3.09818  2.72096  3.02872  3.31033  5.30336  3.94300      6 n - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2....68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03438  3.78314  4.50549  0.61958  0.77255  0.48576  0.95510
+    125   1.15088  4.15203  3.37522  3.16532  3.96636  2.97832  4.19746  3.07892  3.17929  2.96422  4.00830  3.33647  3.70935  3.52940  3.43440  2.50430  2.77559  2.74907  5.40264  4.19344    125 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03438  3.78314  4.50549  0.61958  0.77255  0.48576  0.95510
+    126   2.88010  4.96556  2.45825  1.15999  4.30138  3.21969  3.80228  3.73756  2.67182  3.37042  4.35121  2.89011  3.82087  3.02166  3.06918  2.87345  3.18461  3.43173  5.49013  4.21538    126 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03438  3.78314  4.50549  0.61958  0.77255  0.48576  0.95510
+    127   2.36929  4.21326  3.35308  3.10406  3.89402  3.05467  4.12762  3.01046  3.04521  2.87697  3.93552  3.32607  3.75234  3.44525  3.30664  2.56985  1.33320  2.71507  5.33993  4.11143    127 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03438  3.78314  4.50549  0.61958  0.77255  0.48576  0.95510
+    128   2.36929  4.21326  3.35308  3.10406  3.89402  3.05467  4.12762  3.01046  3.04521  2.87697  3.93552  3.32607  3.75234  3.44525  3.30664  2.56985  1.33320  2.71507  5.33993  4.11143    128 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03438  3.78314  4.50549  0.61958  0.77255  0.48576  0.95510
+    129   2.90890  4.74936  3.39087  2.92422  4.08130  3.41071  3.76730  3.61893  2.21292  3.15138  4.15641  3.28956  3.91991  2.99429  1.12456  2.99885  3.18246  3.34737  5.20214  4.03057    129 r - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03438  3.78314  4.50549  0.61958  0.77255  0.48576  0.95510
+    130   2.36929  4.21326  3.35308  3.10406  3.89402  3.05467  4.12762  3.01046  3.04521  2.87697  3.93552  3.32607  3.75234  3.44525  3.30664  2.56985  1.33320  2.71507  5.33993  4.11143    130 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03438  3.78314  4.50549  0.61958  0.77255  0.48576  0.95510
+    131   2.73804  4.30808  3.99916  3.66215  3.48755  3.62843  4.48014  2.06428  3.52841  2.19218  3.46911  3.86552  4.19579  3.89586  3.74899  3.12843  3.10298  1.14626  5.25593  3.98076    131 v - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03438  3.78314  4.50549  0.61958  0.77255  0.48576  0.95510
+    132   2.90890  4.74936  3.39087  2.92422  4.08130  3.41071  3.76730  3.61893  2.21292  3.15138  4.15641  3.28956  3.91991  2.99429  1.12456  2.99885  3.18246  3.34737  5.20214  4.03057    132 r - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02327  3.77203        *  0.61958  0.77255  0.00000        *
+//

data/amrfinder/AMR.LIB

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR.LIB.h3f

data/amrfinder/AMR.LIB

Binary file data/amrfinder/AMR.LIB.h3f has changed

data/amrfinder/AMR.LIB

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR.LIB.h3i

data/amrfinder/AMR.LIB

Binary file data/amrfinder/AMR.LIB.h3i has changed

data/amrfinder/AMR.LIB

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR.LIB.h3m

data/amrfinder/AMR.LIB

Binary file data/amrfinder/AMR.LIB.h3m has changed

data/amrfinder/AMR.LIB

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR.LIB.h3p

data/amrfinder/AMR.LIB

Binary file data/amrfinder/AMR.LIB.h3p has changed

data/amrfinder/AMRProt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMRProt

data/amrfinder/AMRProt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMRProt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,35202 @@
+>1000903631|WP_061154665.1|1|1|blaLEN-42|blaLEN|hydrolase|class_A_beta-lactamase_LEN-42
+MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARV
+DAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITMSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDR
+WETALNEALPGDMRDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARG
+IVALLGPDGKAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR
+>1000909371|WP_061158039.1|1|1|blaTEM-156|blaTEM|hydrolase|class_A_beta-lactamase_TEM-156
+MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLS
+RVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRL
+DRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGS
+RGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
+>1001043515|WP_061189306.1|1|1|blaPDC-114|blaPDC|hydrolase|class_C_beta-lactamase_PDC-114
+MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV
+TPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD
+YYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAG
+PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL
+QPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR
+>1001044756|WP_061190338.1|1|1|blaPDC-226|blaPDC|hydrolase|class_C_beta-lactamase_PDC-226
+MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV
+TPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD
+YYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVG
+PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL
+QPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR
+>1001048246|WP_061193023.1|1|1|blaPDC-116|blaPDC|hydrolase|class_C_beta-lactamase_PDC-116
+MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV
+TPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD
+YYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAG
+PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL
+QPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR
+>1001048721|WP_061193431.1|1|1|blaPDC-298|blaPDC|hydrolase|class_C_beta-lactamase_PDC-298
+MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV
+TPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD
+YYRQWQPTYAPGSQRLYSNPSISLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAG
+PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL
+QPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR
+>1001056857|WP_061196139.1|1|1|blaPDC-97|blaPDC|hydrolase|class_C_beta-lactamase_PDC-97
+MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV
+TPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD
+YYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAG
+PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL
+QPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR
+>1001067679|WP_061199990.1|1|1|blaPDC-184|blaPDC|hydrolase|class_C_beta-lactamase_PDC-184
+MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV
+TPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD
+YYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRVG
+PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL
+QPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR
+>100173053|ABF69110.1|1|1|beta-4|beta-4||intimin_type_beta
+MITHGFYARTRHKHKLKKTFIMLSAGLGLFFYVNQNSFANGENYFKLGSDSKLLTHNSY..YQELLKFIADLEDILARPERVIEIIKTELNDVRTKFG
+DARRTELLVGEVLSLEDEDLIEEEEVVITLTNNGYIKRMANSEFRAQRRGGRGVQGMGVHDDDFVKNLVSCSTHDTLLFF
+TNTGKVYRAKGYEIPEYGRTAKGIPVINLLGIDSAEKIQAIISVEGKAEAGKYLFFTTLKGTVKRTAVTAFSNIRSNGLI
+AISLKEDDELVNVVTTNGNQKMIIGTHAGYSVTFDENTVRDMGRTASGVRGIRLRENDYVVGAAILDENKEVLVITENGY
+GKRTKASEYPVKGRGGKGIKTANITEKNGPLAGLTTVNGDEDILLITNKGVIIRFNVDSVSQTGRATLGVRLMRMEDGAK
+VVTMAVVEPEEVEEEIVEVVETTKNETTSETEE
+>769549125|WP_002779062.1|1|1|gyrA|gyrA|mutation|DNA_gyrase_subunit_A_GyrA
+MENIFNKDSDIELIDIENSIKSSYLDYSMSVIIGRALPDARDGLKPVHRRILYAMNDLGVGSRSAYKKSARIVGDVIGKY
+HPHGDTAVYDALVRMAQDFSMRYPSIDGQGNFGSIDGDGAAAMRYTEARMTILAEELLRDIDKDTVDFVPNYDDSMSEPD
+VLPARVPNLLLNGSSGIAVGMATNIPPHSLNELVDGLLYLLDHKDASLEDLMQFIKGPDFPTGGIIYGKKGIIEAYRTGR
+GRVKIRAKTHIEKKSNKDIIVIDELPYQTNKARLIEQIAELVKEKQIEGISEVRDESDREGIRVVIELKREAMSEIVLNN
+LFKSTTMESTFGVIMLAIHNKEPKIFSLIELLNLFLNHRKTVIIRRTIFELQKARARAHILEGLKIALDNIDEVIALIKN
+SPDNTTARDSLVAKFGLTELQANAILDMKLGRLTGLEREKIENELAELMKEIARLDEILKSETLLENLIRDELKEIKSKF
+DVPRITQIEDDYDDIDIEDLIPNENMVVTITHRGYIKRVPSKQYEKQKRGGKGKLAVTTYDDDFIESFFTANTHDTLMFV
+TDRGQLYWLKVYKIPEGSRTAKGKAVVNLINLQADEKIMAIIPTTDFDENKSLCFFTKNGIVKRTNLSEYQNIRSVGVKA
+INLDENDELVTAIIVQRDENEETGLLDDDSLNDENTNSDENLIESIKGKMLFAVTKKGMCIKFPLAKVREIGRVSRGVTA
+IKFKEKNDELVGAVVIENDEQEILSISAKGIGKRTNAGEYRLQSRGGKGVICMKLTDKTKELISVVIVDESMDLMALTSS
+GKMIRVDMQSIRKAGRNTSGVIVVNVENDEVVSIAKCPKEELEDEISDENLDLNL
+>769549802|WP_002779996.1|1|1|50S_L22|50S_L22|mutation|50S_ribosomal_protein_L22
+MSKALIKFIRLSPTKARLIAREVQGMNAELAMASLKFMPNKGAKYIANAISSAVANGGFEANEVVVKSCRVDAGAVLKRF
+RPRARGSASRIRKPTSHILVEVAKAEVKTEAKKAVAKKTPVKKTSTKKVTAEKES
+>85676345|WP_000072067.1|1|1|gyrB|gyrB|mutation|DNA_topoisomerase_(ATP-hydrolyzing)_subunit_B_GyrB
+MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPT
+GIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGET
+EKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNI
+FYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLI
+AVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDL
+AGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGR
+DEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIA
+LDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDK
+EQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFE
+QALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAA
+NIDI
+>87081927|WP_000843414.1|1|1|marR|marR|mutation|transcriptional_regulator_MarR
+MKSTSDLFNEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC
+KGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQELTKNLTADEVATLEYLLKKVLP
+>941950587|WP_002289473.1|1|1|cls|cls|mutation|cardiolipin_synthase_Cls
+MVSSIITALYLLNALIALVAILIKPRDVAAIWAWLLVLFALPGVGFVLYLFFGRGLTDKKKFYLRQSDLKELENFQSFRG
+DTIEHYDPDMGDKDKQQFVDFFSSLNRMPLTRMNSVTLLTDGQEKLDSLLQDLKKAKHSIHIEYYAFVTDNIGQQVLHVL
+EEKAAEGVEVRILYDAFGSHGTKAKDFNRLIKNGGHVHTFVTSQRALLRFRLNYHDHRKIVVIDGKISYTGGFNIANQYV
+NTTKKFGYWRDTHIRIFGAASSLLQLRFLTDWNVSVPEEKKVGYHLNYFFKKADRDESKLADTSIQLVSSGPNNEREQIK
+LSFIKLITSAKKRVWIQTPYLVPDESVIAALKIATASGVDVKIMIPNKPDHPFIYRATQYYARQLIKENVQILVYENGFL
+HAKTLIMDDEICMVGSANQDIRSYRLNFETSAVIYDPEFLEELATQFKEDETHCSSMTTETVKEMSNWLLFKQQISRLFS
+PIL
+>949628753|WP_057042458.1|1|1|rpsL|rpsL|mutation|30S_ribosomal_protein_S12_RpsL
+MPTINQLVRKERKKVLEKSKSPALKNCPQRRGVCTRVYTTTPKKPNSALRKVAKVRLTSGFEVISYIGGEGHNLQEHSIV
+LVRGGRVKDLPGVKYHIVRGALDTAGVAKRTVSRSKYGAKRSKAGAAK
+>985479976|WP_002295408.1|1|1|liaF|liaF|mutation|three-component_signaling_pathway_regulator_LiaF
+MNSSWRFFVVVEALLLLFAVWQIVNNTGLLLLVIFGIFNIYLAMRKYPRTKFQNFQLILGSLVIFFSLVNSPALWMMVVL
+AVLFIGLKGVEISGIDLTKNAFWRKKQIMMVQTEQLKTHNNERKRQQLFGNQRIGNDVYEWDDINIAIISGDTIIDLGNT
+LLPKDDNIVIVRKGIGRTRILVPLGVAIRLEHATLVGNVLFEEEQFSLKNEQIKICSSDYDENPRRLKIITNTLVGDVEV
+IRI
+>489000713|WP_002911375.1:47:mgrB_W47R|1|1|mgrB|mgrB|mutation|PhoP/PhoQ_regulator_MgrB
+MKKLRWVLLIVIIAGCLLLWTQMLNVMCDQDVQFFSGICTINKFIPR

data/amrfinder/AMRProt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMRProt-mutation.tab

data/amrfinder/AMRProt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMRProt-mutation.tab Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,416 @@
+#taxgroup accession_version mutation_position mutation_symbol class subclass mutated_protein_name
+Escherichia WP_000019358.1 12 soxS_A12S MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE Escherichia_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS
+Salmonella WP_000019483.1 52 soxS_E52K MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE Salmonella_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS
+Escherichia WP_000031783.1 121 tufA_L121Q POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 125 tufA_Q125E POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 125 tufA_Q125K POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 125 tufA_Q125R POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 161 tufA_Y161C POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 161 tufA_Y161D POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 161 tufA_Y161N POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 231 tufA_R231C POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 231 tufA_R231V POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 234 tufA_R234F POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 234 tufA_R234S POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 317 tufA_G317D POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 330 tufA_Q330H POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 334 tufA_R334C POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 335 tufA_T335A POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 376 tufA_A376S POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 376 tufA_A376T POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 376 tufA_A376V POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 379 tufA_E379K POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Salmonella WP_000072047.1 421 gyrB_Y421C QUINOLONE QUINOLONE Salmonella_quinolone_resistant_GyrB
+Salmonella WP_000072047.1 438 gyrB_R438L QUINOLONE QUINOLONE Salmonella_quinolone_resistant_GyrB
+Salmonella WP_000072047.1 464 gyrB_S464F QUINOLONE CIPROFLOXACIN Salmonella_ciprofloxacin_resistant_GyrB
+Salmonella WP_000072047.1 464 gyrB_S464T QUINOLONE CIPROFLOXACIN Salmonella_ciprofloxacin_resistant_GyrB
+Salmonella WP_000072047.1 464 gyrB_S464Y QUINOLONE CIPROFLOXACIN Salmonella_ciprofloxacin_resistant_GyrB
+Salmonella WP_000072047.1 466 gyrB_E466D QUINOLONE QUINOLONE Salmonella_quinolone_resistant_GyrB
+Escherichia WP_000072067.1 136 gyrB_R136C AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 gyrB_R136E AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 gyrB_R136G AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 gyrB_R136H AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 gyrB_R136I AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 gyrB_R136L AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 gyrB_R136S AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_00007..3 nfsA_R203L NITROFURAN NITROFURANTOIN Escherichia_nitrofurantoin_resistant_NfsA
+Escherichia WP_094970923.1 15 basR_G15R COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 39 basR_S39I COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 basR_G53A COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 basR_G53C COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 basR_G53E COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 basR_G53R COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 basR_G53S COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 basR_G53V COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 basR_G53W COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 81 basR_R81L COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 81 basR_R81S COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 105 basR_L105P COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Klebsiella WP_101982161.1 80 parC_S80I QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_ParC
+Klebsiella WP_101982161.1 84 parC_E84K QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_ParC
+Enterococcus_faecium WP_115256011.1 82 parC_S80I QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_ParC
+Enterococcus_faecium WP_115256011.1 82 parC_S80R QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_ParC
+Enterococcus_faecium WP_115256011.1 86 parC_E84A QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_ParC
+Enterococcus_faecium WP_115256011.1 86 parC_E84K QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_ParC
+Enterococcus_faecium WP_115256011.1 86 parC_E84T QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_ParC
+Klebsiella WP_117036963.1 83 gyrA_S83F QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Klebsiella WP_117036963.1 83 gyrA_S83I QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Klebsiella WP_117036963.1 83 gyrA_S83L QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Klebsiella WP_117036963.1 83 gyrA_S83T QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Klebsiella WP_117036963.1 83 gyrA_S83Y QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Klebsiella WP_117036963.1 87 gyrA_D87A QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Klebsiella WP_117036963.1 87 gyrA_D87G QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Klebsiella WP_117036963.1 87 gyrA_D87H QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Klebsiella WP_117036963.1 87 gyrA_D87N QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Klebsiella WP_117036963.1 87 gyrA_D87Y QUINOLONE QUINOLONE Klebsiella_quinolone_resistant_GyrA
+Enterococcus_faecium WP_137277832.1 84 gyrA_S83I QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_GyrA
+Enterococcus_faecium WP_137277832.1 84 gyrA_S83L QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_GyrA
+Enterococcus_faecium WP_137277832.1 84 gyrA_S83N QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_GyrA
+Enterococcus_faecium WP_137277832.1 84 gyrA_S83R QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_GyrA
+Enterococcus_faecium WP_137277832.1 84 gyrA_S83Y QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_GyrA
+Enterococcus_faecium WP_137277832.1 88 gyrA_E87G QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_GyrA
+Enterococcus_faecium WP_137277832.1 88 gyrA_E87K QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_GyrA
+Enterococcus_faecium WP_137277832.1 88 gyrA_E87L QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_GyrA
+Enterococcus_faecium WP_137277832.1 98 gyrA_S97N QUINOLONE QUINOLONE Enterococcus_faecium_quinolone_resistant_GyrA

data/amrfinder/AMRProt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMRProt-point_mut.tab

data/amrfinder/AMRProt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMRProt-point_mut.tab Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,285 @@
+Escherichia WP_000019358.1 12 S soxS_A12S soxS_A12S MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE Escherichia_multidrug_resistant_SoxS
+Salmonella WP_000019483.1 52 K soxS_E52K soxS_E52K MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE Salmonella_multidrug_resistant_SoxS
+Escherichia WP_000031783.1 121 Q tufA_L121Q tufA_L121Q POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 125 E tufA_Q125E tufA_Q125E POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 125 K tufA_Q125K tufA_Q125K POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 125 R tufA_Q125R tufA_Q125R POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 161 C tufA_Y161C tufA_Y161C POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 161 D tufA_Y161D tufA_Y161D POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 161 N tufA_Y161N tufA_Y161N POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 231 C tufA_R231C tufA_R231C POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 231 V tufA_R231V tufA_R231V POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 234 F tufA_R234F tufA_R234F POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 234 S tufA_R234S tufA_R234S POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 317 D tufA_G317D tufA_G317D POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 330 H tufA_Q330H tufA_Q330H POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 334 C tufA_R334C tufA_R334C POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 335 A tufA_T335A tufA_T335A POLYKETIDE PULVOMYCIN Escherichia_pulvomycin_resistant_TufA
+Escherichia WP_000031783.1 376 S tufA_A376S tufA_A376S POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 376 T tufA_A376T tufA_A376T POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 376 V tufA_A376V tufA_A376V POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Escherichia WP_000031783.1 379 K tufA_E379K tufA_E379K POLYKETIDE KIRROMYCIN Escherichia_kirromycin_resistant_TufA
+Salmonella WP_000072047.1 421 C gyrB_Y421C gyrB_Y421C QUINOLONE QUINOLONE Salmonella_quinolone_resistant_GyrB
+Salmonella WP_000072047.1 438 L gyrB_R438L gyrB_R438L QUINOLONE QUINOLONE Salmonella_quinolone_resistant_GyrB
+Salmonella WP_000072047.1 464 F gyrB_S464F gyrB_S464F QUINOLONE QUINOLONE Salmonella_quinolone_resistant_GyrB
+Salmonella WP_000072047.1 464 Y gyrB_S464Y gyrB_S464Y QUINOLONE QUINOLONE Salmonella_quinolone_resistant_GyrB
+Salmonella WP_000072047.1 466 D gyrB_E466D gyrB_E466D QUINOLONE QUINOLONE Salmonella_quinolone_resistant_GyrB
+Escherichia WP_000072067.1 136 C gyrB_R136C gyrB_R136C AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 E gyrB_R136E gyrB_R136E AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 G gyrB_R136G gyrB_R136G AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 H gyrB_R136H gyrB_R136H AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 I gyrB_R136I gyrB_R136I AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 L gyrB_R136L gyrB_R136L AMINOCOUMARIN AMINOCOUMARIN Escherichia_aminocoumarin_resistant_GyrB
+Escherichia WP_000072067.1 136 S gyr..57904.1 85 Y gyrA_D85Y gyrA_D85Y QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_002857904.1 86 A gyrA_T86A gyrA_T86A QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_002857904.1 86 I gyrA_T86I gyrA_T86I QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_002857904.1 86 K gyrA_T86K gyrA_T86K QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_002857904.1 86 V gyrA_T86V gyrA_T86V QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_002857904.1 90 A gyrA_D90A gyrA_D90A QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_002857904.1 90 N gyrA_D90N gyrA_D90N QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_002857904.1 90 T gyrA_D90T gyrA_D90T QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_002857904.1 90 Y gyrA_D90Y gyrA_D90Y QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_002857904.1 104 S gyrA_P104S gyrA_P104S QUINOLONE QUINOLONE Campylobacter_quinolone_resistant_GyrA
+Campylobacter WP_057042458.1 43 R rpsL_K43R rpsL_K43R AMINOGLYCOSIDE STREPTOMYCIN Campylobacter_streptinomycin_resistant_RpsL
+Campylobacter WP_057042458.1 88 E rpsL_K88E rpsL_K88E AMINOGLYCOSIDE STREPTOMYCIN Campylobacter_streptinomycin_resistant_RpsL
+Campylobacter WP_057042458.1 88 Q rpsL_K88Q rpsL_K88Q AMINOGLYCOSIDE STREPTOMYCIN Campylobacter_streptinomycin_resistant_RpsL
+Campylobacter WP_057042458.1 88 R rpsL_K88R rpsL_K88R AMINOGLYCOSIDE STREPTOMYCIN Campylobacter_streptinomycin_resistant_RpsL
+Escherichia WP_089631889.1 15 C nfsA_R15C nfsA_R15C NITROFURAN NITROFURAN Escherichia_nitrofurantoin_resistant_NfsA
+Escherichia WP_089631889.1 33 R nfsA_S33R nfsA_S33R NITROFURAN NITROFURAN Escherichia_nitrofurantoin_resistant_NfsA
+Escherichia WP_089631889.1 44 * nfsA_Q44STOP nfsA_Q44STOP NITROFURAN NITROFURAN Escherichia_nitrofurantoin_resistant_NfsA
+Escherichia WP_089631889.1 131 D nfsA_G131D nfsA_G131D NITROFURAN NITROFURAN Escherichia_nitrofurantoin_resistant_NfsA
+Escherichia WP_089631889.1 133 S nfsA_R133S nfsA_R133S NITROFURAN NITROFURAN Escherichia_nitrofurantoin_resistant_NfsA
+Escherichia WP_089631889.1 141 * nfsA_K141STOP nfsA_K141STOP NITROFURAN NITROFURAN Escherichia_nitrofurantoin_resistant_NfsA
+Escherichia WP_089631889.1 203 C nfsA_R203C nfsA_R203C NITROFURAN NITROFURAN Escherichia_nitrofurantoin_resistant_NfsA
+Escherichia WP_089631889.1 203 L nfsA_R203L nfsA_R203L NITROFURAN NITROFURAN Escherichia_nitrofurantoin_resistant_NfsA
+Escherichia WP_094970923.1 15 R basR_G15R basR_G15R COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 39 I basR_S39I basR_S39I COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 A basR_G53A basR_G53A COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 C basR_G53C basR_G53C COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 E basR_G53E basR_G53E COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 R basR_G53R basR_G53R COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 S basR_G53S basR_G53S COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 V basR_G53V basR_G53V COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 53 W basR_G53W basR_G53W COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 81 L basR_R81L basR_R81L COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 81 S basR_R81S basR_R81S COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_094970923.1 105 P basR_L105P basR_L105P COLISTIN COLISTIN Escherichia_colistin_resistant_BasR
+Escherichia WP_097509477.1 620 C acrB_R620C acrB_R620C TETRACYCLINE TIGECYCLINE Escherichia_tigecycline_resistant_AcrB

data/amrfinder/AMRProt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMRProt-suppress

data/amrfinder/AMRProt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMRProt-suppress Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,17 @@
+#taxgroup protein_gi
+Escherichia 151858
+Escherichia 151859
+Escherichia 1061418
+Escherichia 2879920
+Escherichia 2879921
+Escherichia 85675040
+Escherichia 85676145
+Escherichia 85676370
+Escherichia 85676543
+Klebsiella 2879921
+Klebsiella 20152201
+Klebsiella 150954280
+Salmonella 85676145
+Staphylococcus 150728
+Staphylococcus 155345
+Vibrio_cholerae 146314413

data/amrfinder/AMRProt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMRProt.phr

data/amrfinder/AMRProt

Binary file data/amrfinder/AMRProt.phr has changed

data/amrfinder/AMRProt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMRProt.pin

data/amrfinder/AMRProt

Binary file data/amrfinder/AMRProt.pin has changed

data/amrfinder/AMRProt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMRProt.psq

data/amrfinder/AMRProt

Binary file data/amrfinder/AMRProt.psq has changed

data/amrfinder/AMR_CDS

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_CDS

data/amrfinder/AMR_CDS

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMR_CDS Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,86699 @@
+>1000903631|WP_061154665.1|NG_066705.1|1|1|blaLEN-42|blaLEN|class_A_beta-lactamase_LEN-42 NG_066705.1:1-861
+atgcgttatgttcgcctgtgtgttatctccctgttagccaccctgccactggcggtatacgccggtccacagccgctaga
+gcagattaaacaaagcgaaagccagctgtcgggccgcgtggggatggtggaaatggatctggccagcggccgcacgctgg
+ctgcctggcgcgccgatgaacgctttcccatggtgagcacctttaaagtgctgctgtgcggcgcggtgctggcgcgggtg
+gatgccggggtcgaacaactggatcggcggatccactaccgccagcaggatctggtggactactccccggtcagcgaaaa
+acaccttgtcgacgggatgacgatcggcgaactctgcgccgccgccatcaccatgagcgataacagcgccggaaatctgc
+tgctggccaccgtcggcggccccgcgggattgaccgcctttctgcgtcagatcggtgacaacgtcacccgtcttgaccgc
+tgggaaacggcactgaatgaggcgcttcccggcgacatgcgcgacaccactaccccggccagcatggccgccacgctgcg
+taaactactgaccgcgcagcatctgagcgcccgttcacagcagcagctcctgcagtggatggtggacgatcgggttgccg
+gcccgctgatccgcgccgtgctgccggcgggctggtttatcgccgacaagaccggggctggcgaacggggtgcgcgcggc
+attgtcgccctgctcggcccggacggcaaagcggagcgcatcgtggtgatctacctgcgggataccccggcgagtatggc
+cgagcgtaatcaacatatcgccgggatcggcgcagcgctgatcgagcactggcaacgctaa
+>1000909371|WP_061158039.1|NG_050200.1|1|1|blaTEM-156|blaTEM|class_A_beta-lactamase_TEM-156 NG_050200.1:101-961
+atgagtattcaacatttccgtgtcgcccttattcccttttttgcggcattttgccttcctgtttttgctcacccagaaac
+gctggtgaaagtaaaagatgctgaagatcagttgggtgcacgagtgggttacatcgaactggatctcaacagcggtaaga
+tccttgagagttttcgccccgaagaacgttttccaatgatgagcacttttaaagttctgctatgtggcgcggtattatcc
+cgtgttgacgccgggcaagagcaactcggtcgccgcatacactattctcagaatgacttggttgagtactcaccagtcac
+agaaaagcatcttacggatggcatgacagtaagagaattatgcagtgctgccataaccatgagtgataacactgcggcca
+acttacttctgacaacgatcggaggaccgaaggagctaaccgcttttttgcacaacataggggatcatgtaactcgcctt
+gatcgttgggaaccggagctgaatgaagccataccaaacgacgagcgtgacaccacgatgcctgcagcaatggcaacaac
+gttgcgcaaactattaactggcgaactacttactctagcttcccggcaacaattaatagactggatggaggcggataaag
+ttgcaggaccacttctgcgctcggcccttccggctggctggtttattgctgataaatctggagccggtgagcgtgggtct
+cgcggtatcattgcagcactggggccagatggtaagccctcccgtatcgtagttatctacacgacggggagtcaggcaac
+tatggatgaacgaaatagacagatcgctgagataggtgcctcactgattaagcattggtaa
+>1001043515|WP_061189306.1|NG_055478.1|1|1|blaPDC-114|blaPDC|class_C_beta-lactamase_PDC-114 NG_055478.1:1-1194
+atgcgcgataccagattcccctgcctgtgcggcatcgccgcttccacactgctgttcgccaccaccccggccattgccgg
+cgaggccccggcggatcgcctgaaggcactggtcgacgccgccgtacaaccggtgatgaaggccaatgacattccgggcc
+tggccgtagccatcagcctgaaaggagaaccgcattacttcagctatgggctggcctcgaaagaggacggccgccgggtg
+acgccggagaccctgttcgagatcggctcggtgagcaagaccttcaccgccaccctcgccggctatgccctgacccagga
+caagatgcgcctcgacgaccgcgccagccagcactggccggcactgcagggcagccgcttcgacggcatcagcctgctcg
+acctcgcgacctataccgccggcggcttgccgctgcagttccccgactcggtgcagaaggaccaggcacagatccgcgac
+tactaccgccagtggcagccgacctacgcgccgggcagccagcgcctctattccaacccgagcatcggcctgttcggcta
+tctcgccgcgcgcagcctgggccagccgttcgaacggctcatggagcagcaagtgttcccggcactgggcctcgaacaga
+cccacctcgacgtgcccgaggcggcgttggcgcagtacgcccagggctacggcaaggacgaccgcccgctacgggccggt
+cccggcccgctggatgccgaaggctacggggtgaagaccagcgcggccgacctgctgcgcttcgtcgatgccaacctgca
+tccggagcgcctggacaggccctgggcgcaggcgctcgatgccacccatcgcggttactacaaggtcggcgacatgaccc
+agggcctgggctgggaagcctacgactggccgatctccctgaagcgcctgcaggccggcaactcgacgccgatggcgctg
+caaccgcacaggatcgccaggctgcccgcgccacaggcgctggagggccagcgcctgctgaacaagaccggttccaccaa
+cggcttcggcgcctacgtggcgttcgtcccgggccgcgacctgggactggtgatcctggccaaccgcaactatcccaatg
+ccgagcgggtgaagatcgcctacgccatcctcagcggcctggagcagcagggcaaggtgccgctgaagcgctga
+>1001044756|WP_061190338.1|NG_056104.1|1|1|blaPDC-226|blaPDC|class_C_beta-lactamase_PDC-226 NG_056104.1:1-1194
+atgcgcgataccagattcccctgcctgtgcggcatcgccgcttccacactgctgttcgccaccaccccggccattgccgg
+cgaggccccggcggatcgcctgaaggcactggtcgacgccgccgtacaaccggtgatgaaggccaatgacattccgggcc
+tggccgtagccatcagcctgaaaggagaaccgcattacttcagctatgggctggcctcgaaagaggacggccgccgggtg
+acgccggagaccctgttcgagatcggctcggtgagcaagaccttcaccgccaccctcgccggctatgccctgacccagga
+caagatgcgcctcgacgaccgcgccagccagcactggccggcactgcagggcagccgcttcgacggcatcagcctgctcg
+acctcgcgacctataccgccggcggct..tgaaaacgc
+ccagactgcgcggcctgctggcactcaacatggccgtagcggcagcgagtgcaatggttatcgtcaacaccgtcgttctg
+gttcaggcggactttggtttctcacagcggtctaccgctattgcgctggccttcttcggcgtggggtccatggtatcggc
+cctggttctccccagactcctcgacaacatgagcgaccgtatgccgatgcttgcaggtacggcgcttttagtcattggcc
+tggggtcaggcattttcctgaaggattacatcacgctggttgtgctctgggcactgctgggggtgggctattcactttct
+cagacaccgggtggtcgcctgctgcgccgttcgtcaacagcggaagacagaccggcgctgtttgccgcccagtttgcact
+gtcacattcatgctggctggtgacttatccgctggccggatgggttggtgcggcatgggggacacaggcttcattcatcg
+ccctgactgttgtggcaacattgtcgctggtcaccgccgtacttatctggcgtcctgagcatgaagtgtacgctcaggtt
+cacagccacaaagacccggaaacaaacaacgaatcgacccatgagcatgatttcgtcattgacgatgaacatccgtcctg
+gccgaagaaagagaagtaa
+>99030338|ABF61435.1|DQ517331.2|1|1|ncrB|ncrB|nickel-sensing_transcriptional_repressor_NcrB DQ517331.2:1480-1749
+atgaccgttcatgcatcacaccctgacattattaaaagacttaaacgtgccgcagggcacctgaaaagtaccatccagat
+gctcgaagatgagaaagcatgtctggatatcgcccagcaactgcacgctgtggaaaaggcgataacgaatgcgaagcgta
+ccttaattcatgaccatctggatcactgcctggaggatgcccttcatgctgaccacacggagtctgataagacgcttagc
+gaatttaaagagataactaaatatctttaa
+>99030340|ABF61437.1|DQ517331.2|1|1|ncrY|ncrY|nickel_resistance_OB_fold_protein_NcrY DQ517331.2:3054-3476
+atggaatctgctatgcaaaaacaatatttcagtcagttcgtcaccggagtgttactcacttcgttcatcgccattcctgc
+tctggcagcgcaaggtggcttctccgcagagaaagagcctgtcgtcactgagcacatgtatgccggtcataaagttcagc
+aggagaatagtcaaagccggattcagatcgtatcgtcaatgcacgaaggggcgtggatcacactggaaggcaatgttgtc
+agccagcagcaggacgagtggtatacgttccgcgacccaaccggtaccatcaaagtccgcatcccgcagaaagtctggaa
+cgggcagcacttcgatgctcaggacctggtacgggtcagtggaccggtaagccatgaaaatgatggttcaattttatatg
+ttgcagttatcagcaaaccctaa
+>9948545|AAG05881.1|AE004091.2|1|1|mexE|mexE|MexE_family_multidrug_efflux_RND_transporter_periplasmic_adaptor_subunit AE004091.2:2808743-2809987
+atggaacagtcatcccacttctcctggcgctaccccctcgcactcgcggccgtactggtcctgagcgcctgcggcaaggc
+cccggaaaccacccaaggcatggcggcgcccaaggtcagcgtcgccgaagtcatcgaacaaccgctgaacgagtgggacg
+aattcaccggccgcctggaggccccggagtcggtggagctgcgcccgcgggtgtcgggctacatcgaccgcgtggccttc
+catgaaggcgcactggtgaagaaaggcgacctgctgttccagatcgacccgcgcccgttcgaggccgaggtcaagcgcct
+cgaagcccagctgcaacaggcccgcgcggcccaggcgcggagcgtcaacgaagcccagcgcggcgaacgcctgcgcgcca
+gcaacgcgatctccgcggaactcgccgacgcccgcaccaccgccgcccaggaagccaaggcggcggtcgccgcgacccag
+gcgcaactggacgcggcgcgcctgaacctgagcttcacccggatcaccgcgccgatcgacggtcgcgtcagccgcgccga
+ggtcaccgccggcaacctggtcaactccggggagaccctgctcaccaccctggtcagcaccgacaaggtctacgcctact
+tcgacgccgacgagcgcgtgttcctcaagtacgtcgagctggcccgccaggccggtcgcgacacgcgcagcgagagcccg
+gtgtacctcggcctgagcagcgaggacggcaacccgcacctgggccggctggacttcctcgacaaccaggtcaacccgcg
+taccggcaccatccgcggccgcgccgtgttcgacaacgccaagggcgagttcaccccgggcctctacgtgcgcctgaagc
+tggtcggcagcaagacctacgccgccaccctgatcaaggacgaagcggtcggcaccgacctgggcaagaagttcgtgctg
+gtcctggatggcgacaacaagaccgtctaccgcaccgtcgagatgggaccgaagctggagggcctgcgcatcgtccgcag
+cggcctgagcaagggcgaccggatcgtcgtgaatggcctgcagcgggtccgcccgggcatgcaggtggatccgcagaagg
+tcgagatggccagcgccgacaccctggccaccctcgcgcgcctgcggcagtcggtcggcgacagcgaaccaccgaaggtg
+gcggcgtccaaggacaacgccactcgcaacgagccgcgcggctga
+>9988580|AAG10695.1|AF254667.1|1|1|perA|perA|BFP_system_transcriptional_regulator_PerA AF254667.1:522-1346
+atgcttacatctaaaaaagaaatgcagagttctgaaaataaacaagaggagaatttagcgttattgttaactaattacat
+ttcatatcagaatatagttatatttacgggggggaatcagtttaagataagaaacaagaaagaattcaccgaatacacaa
+tagaatccaactccttgttttttttagcaaaaaacactcattgggacatggaaattgtcggaatcgataatagtaatccg
+tacagaaaaattataattgatgatgcattaattaagttgctgcattcaatatcatctgatgactcttgttatgtaaaaaa
+aaaaatatttactgcgaacctcaatgaaatgcaattgaatatagtttccaatataattacagacataaaatactcaggca
+acaacaaaaaaatatttaaaatattgtatttattatctttttttaatgattataatgatataattaatgtcatccttagt
+gcttcatctaagagcatcgtacacagggttataaaagtaattgagttggatatatccaaaaactggaaactaggcgatgt
+cagtagttcaatgtttatgagtgattcttgtctgagaaaacaattaaacaaagagaacttaacctttaaaaaaatcatgt
+tagatataaaaatgaaacatgcttctttatttttaagaactactgataaaaacatagatgaaatatcttgtttggttggg
+tttaattccacatcatattttattaaggtatttaaggaatattacaacacaacaccaaaaaaatataatggcgtttattc
+tattacacaaggaacattgccataa

data/amrfinder/AMR_CDS

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_CDS.nhr

data/amrfinder/AMR_CDS

Binary file data/amrfinder/AMR_CDS.nhr has changed

data/amrfinder/AMR_CDS

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_CDS.nin

data/amrfinder/AMR_CDS

Binary file data/amrfinder/AMR_CDS.nin has changed

data/amrfinder/AMR_CDS

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_CDS.nsq

data/amrfinder/AMR_CDS

Binary file data/amrfinder/AMR_CDS.nsq has changed

data/amrfinder/AMR_DNA-Campylobacter

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Campylobacter

data/amrfinder/AMR_DNA-Campylobacter

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMR_DNA-Campylobacter Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,76 @@
+>NC_022347.1@23S_ribosomal_RNA:1040292-1037381
+aaaaaaggtaagctactaagagcgaatggtggatgccttgactggtaaaggcgatgaaggacgtactagactgcgataag
+ctacggggagctgtcaagaagctttgatccgtagatttccgaatggggcaacccaatgtatagagatatacattacctat
+ataggagcgaacgaggggaattgaaacatcttagtaccctcaggaaaagaaatcaatagagattgcgtcagtagcggcga
+gcgaaagcgcaagagggcaaacccagtgcttgcactgggggttgtaggactgcaatgtgcaagaggtaagtttagcagaa
+cattctggaaagtatagccatagagggtgatagtcccgtatgcgaaaaacaaaccttagctagcagtatcctgagtaggg
+cgggacacgagaaatcctgtctgaagctgggtcgaccacgatccaaccctaaatactaataccagatcgatagtgcacaa
+gtaccgtgagggaaaggtgaaaagaactgaggtgatcagagtgaaatagaacctgaaaccatttgcttacaatcattcag
+agccctatgtagcaatacagggtgatggactgccttttgcataatgagcctgcgagttgtggtgtctggcaaggttaagc
+aaacgcgaagccgtagcgaaagcgagtctgaatagggcgcttagtcagatgctgcagacccgaaacgaagtgatctatcc
+atgagcaagttgaagctagtgtaagaactagtggaggactgaacccataggcgttgaaaagccccgggatgacttgtgga
+taggggtgaaaggccaatcaaacttcgtgatagctggttctctccgaaatatatttaggtatagcgttgtgtcgtaatat
+aagggggtagagcactgaatgggctagggcatacaccaatgtaccaaaccctatcaaactccgaataccttatatgtaat
+cacagcagtcaggcggcgagtgataaaatccgtcgtcaagagggaaacaacccagactaccagctaaggtccctaaatct
+tacttaagtggaaaacgatgtgaagttacttaaacaaccaggaggttggcttagaagcagccatcctttaaagaaagcgt
+aatagctcactggtctagtgattttgcgcggaaaatataacggggctaaagtaagtaccgaagctgtagacttgcgcaca
+acttagattatttaagtttagaatatgagaaactaagttatatgtttagttatatttttactgatttttatagagtaaag
+atagaaataaaacttagtaaaatcagtaaaaatattcttagactaaagttaagtagtttaagttgtgtgcaagtggtagg
+agagcgttctatttgcgtcgaaggtataccggtaaggagtgctggagcgaatagaagtgagcatgcaggcatgagtagcg
+ataattaatgtgagaatcattaacgccgtaaacccaaggtttcctacgcgatgctcgtcatcgtagggttagtcgggtcc
+taagtcgagtccgaaaggggtagacgatggcaaattggttaatattccaataccaacattagtgtgcgatggaaggacgc
+ttagggctaagggggctagcggatggaagtgctagtctaaggtcgtaggaggttatacaggcaaatccgtataacaatac
+tccgagaactgaaaggctttttgaagtcttcggatggatagaagaacccctgatgccgtcgagccaagaaaagtttctaa
+gtttagctaatgttgcccgtaccgtaaaccgacacaggtgggtgggatgagtattctaaggcgcgtggaagaactctctt
+taaggaactctgcaaaatagcaccgtatcttcggtataaggtgtggttcgcttcgtattaggatttactccgaaagcgaa
+gaaacttacaacaaagagtccctcccgactgtttaccaaaaacacagcactctgctaactcgtaagaggatgtatagggt
+gtgacgcctgcccggtgctcgaaggttaattgatggggttagcattagcgaagctcttgatcgaagcccgagtaaacggc
+ggccgtaactataacggtcctaaggtagcgaaattccttgtcggttaaataccgacctgcatgaatggcgtaacgagatg
+ggagctgtctcaaagagggatccagtgaaattgtagtggaggtgaaaattcctcctacccgcggcaagacggaaagaccc
+cgtggacctttactacagcttgacactgctatttggataagaatgtgcaggataggtgggaggctttgagtatatgacgc
+cagttgtatatgagccattgttgagataccactctttcttatttgggtagctaaccagcttgagttatcctcaagtggga
+caatgtctggtgggtagtttgactggggcggtcgcctcccaaataataacggaggcttacaaaggttggctcagaacggt
+tggaaatcgttcgtagagtataaaggtataagccagcttaactgcaagacatacaagtcaagcagagacgaaagtcggtc
+ttagtgatccggtggttctgcgtggaagggccatcgctcaaaggataaaaggtaccccggggataacaggctgatctccc
+ccaagagctcacatcgacggggaggtttggcacctcgatgtcggctcatcgcatcctggggctggagcaggtcccaaggg
+tatggctgttcgccatttaaagcggtacgcgagctgggttcagaacgtcgtgagacagttcggtccctatctgccgtggg
+cgtaagaagattgaagagatttgaccctagtacgagaggaccgggttgaacaaaccactggtgtagctgttgttctgcca
+agagcatcgcagcgtagctaagtttggaaagg
+>NC_002163.1@23S_ribosomal_RNA:396449-399360
+agctactaagagcgaatggtggatgccttgactggtaaaggcgatgaaggacgtactagactgcgataagctacggggag
+ctgtcaagaagctttgatccgtagatttccgaatggggcaacccaatgtatagagatatacattacctatataggagcga
+acgaggggaattgaaacatcttagtaccctcaggaaaagaaatcaatagagattgcgtcagtagcggcgagcgaaagcgc
+aagagggcaaacccagtgcttgcactgggggttgtaggactgcaatgtgcaagagctgagtttagcagaacattctggaa
+agtatagccatagagggtgatagtcccgtatgcgaaaaacaaagcttagctagcagtatcctgagtagggcgggacacga
+ggaatcctgtctgaatccgggtcgaccacgatccaaccctaaatactaataccagatcgatagtgcacaagtaccgtgag
+ggaaaggtgaaaagaactgaggtgatcagagtgaaatagaacctgaaaccatttgcttacaatcattcagagcactatgt
+agcaatacagtgtgatggactgccttttgcataatgagcctgcgagttgtggtgtctggcaaggttaagcaaacgcgaag
+ccgtagcgaaagcgagtctgaatagggcgcttagtcagatgctgcagacccgaaacgaagtgatctatccatgagcaagt
+tgaagctagtgtaagaactagtggaggactgaacccataggcgttgaaaagccccgggatgacttgtggataggggtgaa
+aggccaatcaaacttcgtgatagctggttctctccgaaatatatttaggtatagcgttgtgtcgtaatataagggggtag
+agcactgaatgggctagggcatacaccaatgtaccaaaccctatcaaactccgaataccttatatgtaatcacagcagtc
+aggcggcgagtgataaaatccgtcgtcaagagggaaacaacccagactaccagctaaggtccctaaatcttacttaagtg
+gaaaacgatgtgaagttacttaaacaaccaggaggttggcttagaagcagccatcctttaaagaaagcgtaatagctcac
+tggtctagtgattttgcgcggaaaatataacggggctaaagtaagtaccgaagctgtagacttagtttactaagtggtag
+gagagcgttctatttgcgtcgaaggtataccggtaaggagtgctggagcgaatagaagtgagcatgcaggcatgagtagc
+gataattaatgtgagaatcattaacgccgtaaacccaaggtttcctacgcgatgctcgtcatcgtagggttagtcgggtc
+ctaagtcgagtccgaaaggggtagacgatggcaaattggttaatattccaataccaacattagtgtgcgatggaaggacg
+cttagggctaagggggctagcggatggaagtgctagtctaaggtcgtaggaggttatacaggcaaatccgtataacaata
+ctccgagaactgaaaggctttttgaagtcttcggatggatagaagaacccctgatgccgtcgagccaagaaaagtttcta
+agtttagctaatgttgcccgtaccgtaaaccgacacaggtgggtgggatgagtattctaaggcgcgtggaagaactctct
+ttaaggaactctgcaaaatagcaccgtatcttcggtataaggtgtggttagctttgtattaggatttactctgaaagcaa
+ggaaacttacaacaaagagtccctcccgactgtttaccaaaaacacagcactctgctaactcgtaagaggatgtataggg
+tgtgacgcctgcccggtgctcgaaggttaattgatggggttagcattagcgaagctcttgatcgaagcccgagtaaacgg
+cggccgtaactataacggtcctaaggtagcgaaattccttgtcggttaaataccgacctgcatgaatggcgtaacgagat
+gggagctgtctcaaagagggatccagtgaaattgtagtggaggtgaaaattcctcctacccgcggcaagacggaaagacc
+ccgtggacctttactacagcttgacactgctacttggataagaatgtgcaggataggtgggaggctttgagtatatgacg
+ccagttgtatatgagccattgttgagataccactctttcttatttgggtagctaaccagcttgagttatcctcaagtggg
+acaatgtctggtgggtagtttgactggggcggtcgcctcccaaataataacggaggcttacaaaggttggctcagaacgg
+ttggaaatcgttcgtagagtataaaggtataagccagcttaactgcaagacatacaagtcaagcagagacgaaagtcggt
+cttagtgatccggtggttctgtgtggaagggccatcgctcaaaggataaaaggtaccccggggataacaggctgatctcc
+cccaagagctcacatcgacggggaggtttggcacctcgatgtcggctcatcgcatcctggggctggagcaggtcccaagg
+gtatggctgttcgccatttaaagcggtacgcgagctgggttcagaacgtcgtgagacagttcggtccctatctgccgtgg
+gcgtaagaagattgaagagatttgaccctagtacgagaggaccgggttgaacaaaccactggtgtagctgttgttctgcc
+aagagcatcgcagcgtagctaagtttggaaaggataaacgctgaaagcatctaagcgtgaagccaactctaagatgaatc
+ttctctaagctctctagaagactactagtttgataggctgggtgtgtaatggatgaaagtcctttagctgaccagtacta
+atagagcgtttggcttatctttaataaagcat

data/amrfinder/AMR_DNA-Campylobacter

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Campylobacter.nhr

data/amrfinder/AMR_DNA-Campylobacter

Binary file data/amrfinder/AMR_DNA-Campylobacter.nhr has changed

data/amrfinder/AMR_DNA-Campylobacter

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Campylobacter.nin

data/amrfinder/AMR_DNA-Campylobacter

Binary file data/amrfinder/AMR_DNA-Campylobacter.nin has changed

data/amrfinder/AMR_DNA-Campylobacter

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Campylobacter.nsq

data/amrfinder/AMR_DNA-Campylobacter

Binary file data/amrfinder/AMR_DNA-Campylobacter.nsq has changed

data/amrfinder/AMR_DNA-Campylobacter

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Campylobacter.tab

data/amrfinder/AMR_DNA-Campylobacter

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMR_DNA-Campylobacter.tab Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,11 @@
+#accesion_version@gene_name:start-stop mutation_position mutation_symbol class subclass mutated_gene_name
+NC_002163.1@23S_ribosomal_RNA:396449-399360 2074 23S_A2074C MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S
+NC_002163.1@23S_ribosomal_RNA:396449-399360 2074 23S_A2074G MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S
+NC_002163.1@23S_ribosomal_RNA:396449-399360 2074 23S_A2074T MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S
+NC_002163.1@23S_ribosomal_RNA:396449-399360 2075 23S_A2075G MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S
+NC_002163.1@23S_ribosomal_RNA:396449-399360 2627 23S_C2627A MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S
+NC_022347.1@23S_ribosomal_RNA:1040292-1037381 2233 23S_A2074C MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S
+NC_022347.1@23S_ribosomal_RNA:1040292-1037381 2233 23S_A2074G MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S
+NC_022347.1@23S_ribosomal_RNA:1040292-1037381 2233 23S_A2074T MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S
+NC_022347.1@23S_ribosomal_RNA:1040292-1037381 2234 23S_A2075G MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S
+NC_022347.1@23S_ribosomal_RNA:1040292-1037381 2786 23S_C2627A MACROLIDE MACROLIDE Campylobacter_macrolide_resistant_23S

data/amrfinder/AMR_DNA-Escherichia

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Escherichia

data/amrfinder/AMR_DNA-Escherichia

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMR_DNA-Escherichia Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,106 @@
+>NC_000913.3@16S_ribosomal_RNA:4166659-4168201
+aaattgaagagtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaagtcgaacggtaacaggaaga
+agcttgcttctttgctgacgagtggcggacgggtgagtaatgtctgggaaactgcctgatggagggggataactactgga
+aacggtagctaataccgcataacgtcgcaagaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatg
+ggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactgga
+actgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggcgcaagcctgatgcagccatgc
+cgcgtgtatgaagaaggccttcgggttgtaaagtactttcagcggggaggaagggagtaaagttaatacctttgctcatt
+gacgttacccgcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggagggtgcaagcgttaatcggaa
+ttactgggcgtaaagcgcacgcaggcggtttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctga
+tactggcaagcttgagtctcgtagaggggggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaatacc
+ggtggcgaaggcggccccctggacgaagactgacgctcaggtgcgaaagcgtggggagcaaacaggattagataccctgg
+tagtccacgccgtaaacgatgtcgacttggaggttgtgcccttgaggcgtggcttccggagctaacgcgttaagtcgacc
+gcctggggagtacggccgcaaggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaat
+tcgatgcaacgcgaagaaccttacctggtcttgacatccacggaagttttcagagatgagaatgtgccttcgggaaccgt
+gagacaggtgctgcatggctgtcgtcagctcgtgttgtgaaatgttgggttaagtcccgcaacgagcgcaacccttatcc
+tttgttgccagcggtccggccgggaactcaaaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtc
+atcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcgacctcgcgagagcaagcgga
+cctcataaagtgcgtcgtagtccggattggagtctgcaactcgactccatgaagtcggaatcgctagtaatcgtggatca
+gaatgccacggtgaatacgttcccgggccttgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggt
+agcttaaccttcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaacaaggtaaccgtaggggaac
+ctgcggttggatcacctccttac
+>NC_000913.3@16S_ribosomal_RNA:3941808-3943350
+aaattgaagagtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaagtcgaacggtaacaggaaac
+agcttgctgtttcgctgacgagtggcggacgggtgagtaatgtctgggaaactgcctgatggagggggataactactgga
+aacggtagctaataccgcataacgtcgcaagaccaaagagggggaccttcgggcctcttgccatcagatgtgcccagatg
+ggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactgga
+actgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggcgcaagcctgatgcagccatgc
+cgcgtgtatgaagaaggccttcgggttgtaaagtactttcagcggggaggaagggagtaaagttaatacctttgctcatt
+gacgttacccgcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggagggtgcaagcgttaatcggaa
+ttactgggcgtaaagcgcacgcaggcggtttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctga
+tactggcaagcttgagtctcgtagaggggggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaatacc
+ggtggcgaaggcggccccctggacgaagactgacgctcaggtgcgaaagcgtggggagcaaacaggattagataccctgg
+tagtccacgccgtaaacgatgtcgacttggaggttgtgcccttgaggcgtggcttccggagctaacgcgttaagtcgacc
+gcctggggagtacggccgcaaggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaat
+tcgatgcaacgcgaagaaccttacctggtcttgacatccacggaagttttcagagatgagaatgtgccttcgggaaccgt
+gagacaggtgctgcatggctgtcgtcagctcgtgttgtgaaatgttgggttaagtcccgcaacgagcgcaacccttatcc
+tttgttgccagcggtccggccgggaactcaaaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtc
+atcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcgacctcgcgagagcaagcgga
+cctcataaagtgcgtcgtagtccggattggagtctgcaactcgactccatgaagtcggaatcgctagtaatcgtggatca
+gaatgccacggtgaatacgttcccgggccttgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggt
+agcttaaccttcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaacaaggtaaccgtaggggaac
+ctgcggttggatcacctccttac
+>NC_000913.3@16S_ribosomal_RNA:223771-225313
+aaattgaagagtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaagtcgaacggtaacaggaaga
+agcttgcttctttgctgacgagtggcggacgggtgagtaatgtctgggaaactgcctgatggagggggataactactgga
+aacggtagctaataccgcataacgtcgcaagaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatg
+ggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactgga
+actgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggcgcaagcctgatgcagccatgc
+cgcgtgtatgaagaaggccttcgggttgtaaagtactttcagcggggaggaagggagtaaagttaatacctttgctcatt
+gacgttacccgcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggagggt..caaggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaat
+tcgatgcaacgcgaagaaccttacctggtcttgacatccacagaactttccagagatggattggtgccttcgggaactgt
+gagacaggtgctgcatggctgtcgtcagctcgtgttgtgaaatgttgggttaagtcccgcaacgagcgcaacccttatct
+tttgttgccagcggtccggccgggaactcaaaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtc
+atcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcgacctcgcgagagcaagcgga
+cctcataaagtgcgtcgtagtccggattggagtctgcaactcgactccatgaagtcggaatcgctagtaatcgtggatca
+gaatgccacggtgaatacgttcccgggccttgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggt
+agcttaaccttcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaacaaggtaaccgtaggggaac
+ctgcggttggatcacctccttac
+>NC_004431.1@23S_ribosomal_RNA:237160-240064
+ggttaagcgactaagcgtacacggtggatgccctggcagtcagaggcgatgaaggacgtgctaatctgcgataagcgtcg
+gtaaggtgatatgaaccgttataaccggcgatttccgaatggggaaacccagtgtgtttcgacacactatcattaactga
+atccataggttaatgaggcgaaccgggggaactgaaacatctaagtaccccgaggaaaagaaatcaaccgagattccccc
+agtagcggcgagcgaacggggaggagcccagagcctgaatcagtgtgtgtgttagtggaagcgtctggaaaggcgcgcga
+tacagggtgacagccccgtacacaaaaatgcacatgctgtgagctcgatgagtagggcgggacacgtggtatcctgtctg
+aatatggggggaccatcctccaaggctaaatactcctgactgaccgatagtgaaccagtaccgtgagggaaaggcgaaaa
+gaaccccggcgaggggagtgaaaaagaacctgaaaccgtgtacgtacaagcagtgggagcatgcttaggcgtgtgactgc
+gtaccttttgtataatgggtcagcgacttatattctgtagcaaggttaaccgaataggggagccgaagggaaaccgagtc
+ttaactgggcgttaagttgcagggtatagacccgaaacccggtgatctagccatgggcaggttgaaggttgggtaacact
+aactggaggaccgaaccgactaatgttgaaaaattagcggatgacttgtggctgggggtgaaaggccaatcaaaccggga
+gatagctggttctccccgaaagctatttaggtagcgcctcgtgaactcatctccgggggtagagcactgtttcggcaagg
+gggtcatcccgacttaccaacccgatgcaaactgcgaataccggagaatgttatcacgggagacacacggcgggtgctaa
+cgtccgtcgngaagagggaaacaacccagaccgccagctaaggtcccaaagtcatggttaagtgggaaacgatgtgggaa
+ggcccagacagccaggatgttggcttagaagcagccatcatttaaagaaagcgtaatagctcactggtcgagtcggcctg
+cgcggaagatgtaacggggctaaaccatgcaccgaagctgcggcagcgacgcttatgcgttgttgggtaggggagcgttc
+tgtaagcctgtgaaggtgtactgtgaggtatgctggaggtatcagaagtgcgaatgctgacataagtaacgataaagcgg
+gtgaaaagcccgctcgccggaagaccaagggttcctgtccaacgttaatcggggcagggtgagtcgacccctaaggcgag
+gccgaaaggcgtagtcgatgggaaacaggttaatattcctgtacttggtgttactgcgaaggggggacggagaaggctat
+gttggccgggcgacggttgtcccggtttaagcgtgtaggctggttttccaggcaaatccggaaaatcaaggctgaggcgt
+gatgacgaggcactacggtgctgaagcaacaaatgccctgcttccaggaaaagcctctaagcatcaggtaacatcaaatc
+gtaccccaaaccgacacaggtggtcaggtagagaataccaaggcgcttgagagaactcgggtgaaggaactaggcaaaat
+ggtgccgtaacttcgggagaaggcacgctgatatgtaggtgaagcgacttgctcgtggagctgaaatcagtcgaagatac
+cagctggctgcaactgtttattaaaaacacagcactgtgcaaacacgaaagtggacgtatacggtgtgacgcctgcccgg
+tgccggaaggttaattgatggggttagcgcaagcgaagctcttgatcgaagccccggtaaacggcggccgtaactataac
+ggtcctaaggtagcgaaattccttgtcgggtaagttccgacctgcacgaatggcgtaatgatggccaggctgtctccacc
+cgagactcagtgaaattgaactcgctgtgaagatgcagtgtacccgcggcaagacggaaagaccccgtgaacctttacta
+tagcttgacactgaacattgagccttgatgtgtaggataggtgggaggctttgaagtgtggacgccagtctgcatggagc
+cgaccttgaaataccaccctttaatgtttgatgttctaacgttgacccgtaatccgggttgcggacagtgtctggtgggt
+agtttgactggggcggtctcctcctaaagagtaacggaggagcacgaaggttggctaatcctggtcggacatcaggaggt
+tagtgcaatggcataagccagcttgactgcgagcgtgacggcgcgagcaggtgcgaaagcaggtcatagtgatccggtgg
+ttctgaatggaagggccatcgctcaacggataaaaggtactccggggataacaggctgataccgcccaagagttcatatc
+gacggcggtgtttggcacctcgatgtcggctcatcacatcctggggctgaagtaggtcccaagggtatggctgttcgcca
+tttaaagtggtacgcgagctgggtttagaacgtcgtgagacagttcggtccctatctgccgtgggcgctggagaactgag
+gggggctgctcctagtacgagaggaccggagtggacgcatcactggtgttcgggttgtcatgccaatggcactgcccggt
+agctaaatgcggaagagataagtgctgaaagcatctaagcacgaaacttgccccgagatgagttctccctgactccttga
+gggtcctgaaggaacgttgaagacgacgacgttgataggccgggtgtgtaagcgcagcgatgcgttgagctaaccggtac
+taatgaaccgtgaggcttaacctta
+>NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489
+tggctgctatcctgacagttgtcacgctgattggtgtcgttacaatctaacgcatcgccaatgtaaatccggcccgccta
+tggcgggccgttttgtatggaaaccagaccctatgttcaaaacgacgctctgcaccttattaattaccgcctcttgctcc
+acatttgccgcccctcaacaaatcaacgatattgtgcatcgcacaattaccccgcttatagagcaacaaaagatccccgg
+tatgg

data/amrfinder/AMR_DNA-Escherichia

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Escherichia.nhr

data/amrfinder/AMR_DNA-Escherichia

Binary file data/amrfinder/AMR_DNA-Escherichia.nhr has changed

data/amrfinder/AMR_DNA-Escherichia

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Escherichia.nin

data/amrfinder/AMR_DNA-Escherichia

Binary file data/amrfinder/AMR_DNA-Escherichia.nin has changed

data/amrfinder/AMR_DNA-Escherichia

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Escherichia.nsq

data/amrfinder/AMR_DNA-Escherichia

Binary file data/amrfinder/AMR_DNA-Escherichia.nsq has changed

data/amrfinder/AMR_DNA-Escherichia

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Escherichia.tab

data/amrfinder/AMR_DNA-Escherichia

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMR_DNA-Escherichia.tab Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,48 @@
+#accesion_version@gene_name:start-stop mutation_position mutation_symbol class subclass mutated_gene_name
+NC_000913.3@16S_ribosomal_RNA:223771-225313 1192 16S_C1192T AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsH
+NC_000913.3@16S_ribosomal_RNA:3941808-3943350 794 16S_A794G AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC
+NC_000913.3@16S_ribosomal_RNA:3941808-3943350 794 16S_A794T AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC
+NC_000913.3@16S_ribosomal_RNA:3941808-3943350 926 16S_G926A AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC
+NC_000913.3@16S_ribosomal_RNA:3941808-3943350 926 16S_G926C AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC
+NC_000913.3@16S_ribosomal_RNA:3941808-3943350 926 16S_G926T AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC
+NC_000913.3@16S_ribosomal_RNA:3941808-3943350 1519 16S_A1519C AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC
+NC_000913.3@16S_ribosomal_RNA:3941808-3943350 1519 16S_A1519G AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC
+NC_000913.3@16S_ribosomal_RNA:3941808-3943350 1519 16S_A1519T AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 523 16S_A523C AMINOGLYCOSIDE STREPTOMYCIN Escherichia_streptomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 527 16S_G527T AMINOGLYCOSIDE STREPTOMYCIN Escherichia_streptomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 528 16S_C528T AMINOGLYCOSIDE STREPTOMYCIN Escherichia_streptomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 964 16S_A964G TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1053 16S_G1053A TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1054 16S_C1054T TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1055 16S_A1055G TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1058 16S_G1058C TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1064 16S_G1064A AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1064 16S_G1064C AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1064 16S_G1064T AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1066 16S_C1066T AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1068 16S_G1068A AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1192 16S_C1192A AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1192 16S_C1192G AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1192 16S_C1192T AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1406 16S_T1406A AMINGLYCOSIDE G418/TOBRAMYCIN Escherichia_g418/tobramycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1408 16S_A1408G AMINOGLYCOSIDE GENTAMICIN_C/NEOMYCIN/PAROMOMYCIN Escherichia_gentamicin_c/neomycin/paromomycin_resistant_16S_rrsB
+NC_000913.3@16S_ribosomal_RNA:4166659-4168201 1499 16S_A1499G EDEINE EDEINE Escherichia_edeine_resistant_16S_rrsB
+NC_004431.1@23S_ribosomal_RNA:237160-240064 754 23S_T754A MACROLIDE ERYTHROMYCIN/TELITHROMYCIN Escherichia_erythromycin/telithromycin_resistant_23S
+NC_004431.1@23S_ribosomal_RNA:237160-240064 2032 23S_G2032A LINCOSAMIDE/OXAZOLIDINONE CLINDAMYCIN/LINEZOLID Escherichia_clindamycin/linezolid_resistant_23S
+NC_004431.1@23S_ribosomal_RNA:237160-240064 2032 23S_G2032C OXAZOLIDINONE LINEZOLID Escherichia_linezolid_resistant_23S
+NC_004431.1@23S_ribosomal_RNA:237160-240064 2032 23S_G2032T MACROLIDE/OXAZOLIDINONE CLARITHROMYCIN/LINEZOLID Escherichia_clarithromycin/linezolid_resistant_23S
+NC_004431.1@23S_ribosomal_RNA:237160-240064 2057 23S_G2057A MULTIDRUG CHLORAMPHENICOL/ERYTHROMYCIN/TELITHROMYCIN Escherichia_chloramphenicol/erythromycin/telithromycin_resistant_23S
+NC_004431.1@23S_ribosomal_RNA:237160-240064 2058 23S_A2058G MACROLIDE AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN Escherichia_azithromycin/erythromycin/telithromycin_resistant_23S
+NC_004431.1@23S_ribosomal_RNA:237160-240064 2058 23S_A2058T MACROLIDE AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN Escherichia_azithromycin/erythromycin/telithromycin_resistant_23S
+NC_004431.1@23S_ribosomal_RNA:237160-240064 2447 23S_G2447T OXAZOLIDINONE LINEZOLID Escherichia_linezolid_resistant_23S
+NC_004431.1@23S_ribosomal_RNA:237160-240064 2609 23S_T2609C MACROLIDE TELITHROMYCIN Escherichia_telithromycin_resistant_23S
+NC_004431.1@23S_ribosomal_RNA:237160-240064 2611 23S_C2611T MACROLIDE ERYTHROMYCIN/TELITHROMYCIN Escherichia_erythromycin/telithromycin_resistant_23S
+NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489 12 ampC_C-42A BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC
+NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489 12 ampC_C-42G BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC
+NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489 12 ampC_C-42T BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC
+NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489 22 ampC_T-32A BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC
+NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489 22 ampC_T-32C BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC
+NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489 22 ampC_T-32G BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC
+NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489 39 ampC_G-15GG BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC
+NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489 40 ampC_T-14TGT BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC
+NZ_CP041538.1@ampC/blaEC_promoter_region:1149245-1149489 43 ampC_C-11T BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC

data/amrfinder/AMR_DNA-Salmonella

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Salmonella

data/amrfinder/AMR_DNA-Salmonella

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMR_DNA-Salmonella Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,21 @@
+>NC_003197.2@16S_ribosomal_RNA:3570470-3572005
+aggtaaggaggtgatccaaccgcaggttcccctacggttaccttgttacgacttcaccccagtcatgaatcacaaagtgg
+taagcgccctcccgaaggttaagctacctacttcttttgcaacccactcccatggtgtgacgggcggtgtgtacaaggcc
+cgggaacgtattcaccgtggcattctgatccacgattactagcgattccgacttcatggagtcgagttgcagactccaat
+ccggactacgacgcactttatgaggtccgcttgctctcgcgaggtcgcttctctttgtatgcgccattgtagcacgtgtg
+tagccctggtcgtaagggccatgatgacttgacgtcatccccaccttcctccagtttatcactggcagtctcctttgagt
+tcccgacctaatcgctggcaacaaaggataagggttgcgctcgttgcgggacttaacccaacatttcacaacacgagctg
+acgacagccatgcagcacctgtctcacagttcccgaaggcaccaatccatctctggaaagttctgtggatgtcaagacca
+ggtaaggttcttcgcgttgcatcgaattaaaccacatgctccaccgcttgtgcgggcccccgtcaattcatttgagtttt
+aaccttgcggccgtactccccaggcggtctacttaacgcgttagctccggaagccacgcctcaagggcacaacctccaag
+tagacatcgtttacggcgtggactaccagggtatctaatcctgtttgctccccacgctttcgcacctgagcgtcagtctt
+tgtccagggggccgccttcgccaccggtattcctccagatctctacgcatttcaccgctacacctggaattctacccccc
+tctacaagactcaagcctgccagtttcgaatgcagttcccaggttgagcccggggatttcacatccgacttgacagaccg
+cctgcgtgcgctttacgcccagtaattccgattaacgcttgcaccctccgtattaccgcggctgctggcacggagttagc
+cggtgcttcttctgcgggtaacgtcaattgctgcggttattaaccacaacaccttcctccccgctgaaagtactttacaa
+cccgaaggccttcttcatacacgcggcatggctgcatcaggcttgcgcccattgtgcaatattccccactgctgcctccc
+gtaggagtctggaccgtgtctcagttccagtgtggctggtcatcctctcagaccagctagggatcgtcgccttggtgagc
+cgttacctcaccaacaagctaatcccatctgggcacatctgatggcaagaggcccgaaggtccccctctttggtcttgcg
+acgttatgcggtattagccaccgtttccagtagttatccccctccatcaggcagtttcccagacattactcacccgtccg
+ccactcgtcagcgaagcagcaagctgcttcctgttaccgttcgacttgcatgtgttaggcctgccgccagcgttcaatct
+gagccatgatcaaact

data/amrfinder/AMR_DNA-Salmonella

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Salmonella.nhr

data/amrfinder/AMR_DNA-Salmonella

Binary file data/amrfinder/AMR_DNA-Salmonella.nhr has changed

data/amrfinder/AMR_DNA-Salmonella

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Salmonella.nin

data/amrfinder/AMR_DNA-Salmonella

Binary file data/amrfinder/AMR_DNA-Salmonella.nin has changed

data/amrfinder/AMR_DNA-Salmonella

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Salmonella.nsq

data/amrfinder/AMR_DNA-Salmonella

Binary file data/amrfinder/AMR_DNA-Salmonella.nsq has changed

data/amrfinder/AMR_DNA-Salmonella

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/AMR_DNA-Salmonella.tab

data/amrfinder/AMR_DNA-Salmonella

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/AMR_DNA-Salmonella.tab Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,3 @@
+#accesion_version@gene_name:start-stop mutation_position mutation_symbol class subclass mutated_gene_name
+NC_003197.2@16S_ribosomal_RNA:3570470-3572005 1065 16S_C1065T AMINOGLYCOSIDE SPECTINOMYCIN Salmonella_spectinomycin_resistant_16S_rrsD
+NC_003197.2@16S_ribosomal_RNA:3570470-3572005 1192 16S_C1192T AMINOGLYCOSIDE SPECTINOMYCIN Salmonella_spectinomycin_resistant_16S_rrsD

data/amrfinder/ReferenceGeneCatalog.txt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/ReferenceGeneCatalog.txt

data/amrfinder/ReferenceGeneCatalog.txt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/ReferenceGeneCatalog.txt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,6444 @@
+allele gene_family whitelisted_taxa product_name scope type subtype class subclass refseq_protein_accession refseq_nucleotide_accession curated_refseq_start genbank_protein_accession genbank_nucleotide_accession genbank_strand_orientation genbank_cds_start genbank_cds_stop pubmed_reference blacklisted_taxa db_version
+ ble BLMA family bleomycin binding protein core AMR AMR BLEOMYCIN BLEOMYCIN WP_063842967.1 NG_047554.1 No CAA02068.1 A31900.1 + 6 374 2019-10-30.1
+ ble BLMA family bleomycin binding protein core AMR AMR BLEOMYCIN BLEOMYCIN WP_063842962.1 NG_047553.1 No AAB00464.1 L26954.1 + 10 378 2019-10-30.1
+ bla2 BcII family subclass B1 metallo-beta-lactamase core AMR AMR BETA-LACTAM CARBAPENEM WP_000799232.1 NG_055630.1 No AAA22562.1 M19530.1 + 416 1186 2019-10-30.1
+ bla2 BcII family subclass B1 metallo-beta-lactamase core AMR AMR BETA-LACTAM CARBAPENEM WP_000799223.1 NG_047220.1 No AAK53751.1 AF367984.1 + 791 1561 2019-10-30.1
+ bla2 BcII family subclass B1 metallo-beta-lactamase core AMR AMR BETA-LACTAM CARBAPENEM WP_063839879.1 NG_056058.1 No PHG63909.1 NUUO01000028.1 + 82058 82831 2019-10-30.1
+ bla2 BcII family subclass B1 metallo-beta-lactamase core AMR AMR BETA-LACTAM CARBAPENEM WP_063839880.1 NG_047221.1 No AAR20596.1 AY453162.1 + 501 1271 2019-10-30.1
+ bla2 BcII family subclass B1 metallo-beta-lactamase core AMR AMR BETA-LACTAM CARBAPENEM WP_000799227.1 NG_047222.1 No AAT60435.1 AE017355.1 - 3289352 3290122 2019-10-30.1
+ bla2 BcII family subclass B1 metallo-beta-lactamase core AMR AMR BETA-LACTAM CARBAPENEM WP_012261328.1 NG_047224.1 No ABY44328.1 CP000903.1 - 3200936 3201709 2019-10-30.1
+ ampC CMY2/MIR/ACT/EC family class c beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM WP_006178946.1 NG_047383.1 No AAM11666.1 AF492446.1 + 962 2107 2019-10-30.1
+ ampC CMY2/MIR/ACT/EC family class c beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM WP_063406924.1 NG_051160.1 No AAF18992.1 AF211348.1 + 233 1378 2019-10-30.1
+ bcrB quaternary ammonium compound efflux SMR transporter BcrB core STRESS BIOCIDE BACITRACIN BACITRACIN WP_003725293.1 NG_055638.1 No EAL09801.1 AADR01000010.1 + 8151 8468 2019-10-30.1
+ bcrC quaternary ammonium compound efflux SMR transporter BcrC core STRESS BIOCIDE BACITRACIN BACITRACIN WP_003725292.1 NG_055639.1 No EAL09800.1 AADR01000010.1 + 8486 8830 2019-10-30.1
+ smr multidrug efflux SMR transporter Smr core STRESS BIOCIDE MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE WP_063854743.1 NG_048047.1 No AGX26873.1 KF556707.1 + 123 440 2019-10-30.1
+ qac Qac-pB8 family quaternary ammonium compound efflux SMR transporter core STRESS BIOCIDE QUATERNARY AMMONIUM QUATERNARY AMMONIUM WP_011342944.1 NG_048036.1 No CAI10743.1 AJ863570.1 + 7152 7484 2019-10-30.1
+ aac(2')-IIa kasugamycin N-acetyltransferase AAC(2')-IIa core AMR AMR AMINOGLYCOSIDE KASUGAMYCIN WP_063839881.1 NG_047225.1 No BAM16262.1 AB669090.1 + 12439 13221 2019-10-30.1
+ aac(2')-IIb kasugamycin N-acetyltransferase AAC(2')-IIb core AMR AMR AMINOGLYCOSIDE KASUGAMYCIN WP_071224044.1 NG_055672.1 No APB03221.1 KX531051.1 + 1 723 2019-10-30.1
+ aac(2')-Ia aminoglycoside N-acetyltransferase AAC(2')-Ia core AMR AMR AMINOGLYCOSIDE GENTAMICIN/TOBRAMCYIN WP_004918308.1 NG_047226.1 No AAA03550.1 L06156.2 + 264 800 2019-10-30.1
+ aac(2')-Ib aminoglycoside N-acetyltransferase AAC(2')-Ib core AMR AMR AMINOGLYCOSIDE GENTAMICIN/TOBRAMCYIN WP_003881640.1 NG_047227.1 No AAC44793.1 U41471.1 + 265 852 2019-10-30.1
+ aac(2')-Ic aminoglycoside N-acetyltransferase AAC(2')-Ic core AMR AMR AMINOGLYCOSIDE GENTAMICIN/TOBRAMCYIN WP_003899880.1 NG_047229.1 No AAB17563.1 U72714.1 + 373 918 2019-10-30.1
+ aac(2')-Id aminoglycoside N-acetyltransferase AAC(2')-Id core AMR AMR AMINOGLYCOSIDE GENTAMICIN/TOBRAMCYIN WP_011726942.1 NG_047230.1 No AAB41701.1 U..QUINOLONE/RIFAMPIN/TETRACYCLINE WP_000412428.1 No 2019-10-30.1
+soxR_G121D soxR Salmonella redox-sensitive transcriptional activator SoxR core AMR POINT MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE WP_000412686.1 No 2019-10-30.1
+soxR_R20H soxR Escherichia redox-sensitive transcriptional activator SoxR core AMR POINT MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE WP_000412428.1 No 2019-10-30.1
+soxR_R20H soxR Salmonella redox-sensitive transcriptional activator SoxR core AMR POINT MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE WP_000412686.1 No 2019-10-30.1
+soxS_A12S soxS Escherichia regulatory protein SoxS core AMR POINT MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE WP_000019358.1 No 2019-10-30.1
+soxS_E52K soxS Salmonella regulatory protein SoxS core AMR POINT MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE WP_000019483.1 No 2019-10-30.1
+tufA_A376S tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_A376T tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_A376V tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_E379K tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_G317D tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_L121Q tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_Q125E tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_Q125K tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_Q125R tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_Q330H tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_R231C tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE PULVOMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_R231V tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE PULVOMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_R234F tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE PULVOMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_R234S tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE PULVOMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_R334C tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE PULVOMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_T335A tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE PULVOMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_Y161C tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_Y161D tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+tufA_Y161N tufA Escherichia translation elongation factor EF-Tu 1 core AMR POINT POLYKETIDE KIRROMYCIN WP_000031783.1 No 2019-10-30.1
+uhpA_G97D uhpA Escherichia DNA-binding response regulator core AMR POINT FOSFOMYCIN FOSFOMYCIN WP_000633668.1 No 2019-10-30.1
+uhpT_E350Q uhpT Escherichia hexose phosphate transporter core AMR POINT FOSFOMYCIN FOSFOMYCIN WP_000879194.1 No 2019-10-30.1

data/amrfinder/changes.txt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/changes.txt

data/amrfinder/changes.txt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/changes.txt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,4729 @@
+---------------------------------------------------------------------
+Changes included in 2020-01-06.1
+---------------------------------------------------------------------
+
+This update includes backward incompatible changes to the AMRFinderPlus
+database format. It is compatible with AMRFinderPlus version 3.6. To use
+this database version please update to AMRFinderPlus version 3.6.
+See https://github.com/ncbi/amr/wiki/Upgrading for how to upgrade and
+https://github.com/evolarjun/amr/wiki/AMRFinderPlus-database for information
+on the new database format.
+
+Some highlights:
+
+- Database format has changed to allow AMRFinderPlus to detect promoter mutations and small indels
+
+- Many new point mutations, including Escherichia ampC promoter mutations, Klebsiella, and Enterococcus mutations
+
+- Small improvements to many product names
+
+- Improvements in class and subclass phenotype designations
+
+- Modifications and additions of a few HMMs
+
+- The usual addition of new alleles submitted to NCBI and others gleaned from the
+literature
+
+
+
+- Protein and point mutations:
+          Total in prev: 6443
+       Total in release: 6622
+                Removed: 0
+                  Added: 184
+          Protein Added:  ABV01310.1      ltcA            heat-labile_enterotoxin_LT_subunit_A
+          Protein Added:  ADE89421.1      sslE            lipoprotein_metalloprotease_SslE
+          Protein Added:  ASK37426.1      aar             AggR-activated_transcriptional_regulator_Aar
+          Protein Added:  BAB41547.1      mepA            multidrug_efflux_MATE_transporter_MepA
+          Protein Added:  WP_000378442.1  emrR            multidrug_efflux_transporter_EmrAB_transcriptional_repressor_EmrR
+          Protein Added:  WP_001132507.1  acrB            multidrug_efflux_RND_transporter_permease_subunit_AcrB
+          Protein Added:  WP_002289153.1  liaR            response_regulator_transcription_factor_LiaR
+          Protein Added:  WP_002289154.1  liaS            sensor_histidine_kinase_LiaS
+          Protein Added:  WP_002289473.1  cls             cardiolipin_synthase_Cls
+          Protein Added:  WP_002295408.1  liaF            three-component_signaling_pathway_regulator_LiaF
+          Protein Added:  WP_002355137.1  liaR            response_regulator_transcription_factor_LiaR
+          Protein Added:  WP_002356022.1  yybT            cyclic_dinucleotide_phosphodiesterase_YybT
+          Protein Added:  WP_002365182.1  liaS            sensor_histidine_kinase_LiaS
+          Protein Added:  WP_002371880.1  parC            DNA_topoisomerase_IV_subunit_A_ParC
+          Protein Added:  WP_002381168.1  liaF            three-component_signaling_pathway_regulator_LiaF
+          Protein Added:  WP_002389492.1  gshF            bifunctional_glutamate--cysteine_ligase/glutathione_synthetase_GshF
+          Protein Added:  WP_002413481.1  cls             cardiolipin_synthase_Cls
+          Protein Added:  WP_002895659.1  pmrA            two-component_system_response_regulator_PmrA
+          Protein Added:  WP_002911375.1:47:mgrB_W47R mgrB            PhoP/PhoQ_regulator_MgrB
+          Protein Added:  WP_004147969.1  phoQ            two-component_system_sensor_histidine_kinase_PhoQ
+          Protein Added:  WP_004150807.1  phoP            two-component_system_response_regulator_PhoP
+          Protein Added:  WP_004179093.1  pmrB            two-component_system_sensor_histidine_kinase_PmrB
+          Protein Added:  WP_004184324.1  crrB            HAMP_domain-containing_histidine_kinase_CrrB
+          Protein Added:  WP_014906821.1  arnC            undecaprenyl-phosphate_4-deoxy-4-formamido-L-arabinose_transferase_ArnC
+          Protein Added:  WP_033554192.1  parE            DNA_topoisomerase_IV_subunit_B_ParE
+          Protein Added:  WP_033785346.1  gyrA            DNA_gyrase_subunit_..         HMM Removed:  NF000391.1      EmrB
+            HMM Removed:  NF010314.2      PRK13751.2
+            HMM Removed:  NF012135.0      ANT_3pp_9_crypt
+            HMM Removed:  NF012144.2      ramA_TF
+            HMM Removed:  NF012163.2      BaeS_SmeS
+            HMM Removed:  NF012168.1      BlaI_of_BCL
+            HMM Removed:  NF012198.0      MarA_TF
+            HMM Removed:  NF012208.0      SDR_dihy_bifunc
+            HMM Removed:  NF012226.0      AdeS_HK
+            HMM Removed:  NF012227.0      AdeR_RR
+            HMM Removed:  NF012228.1      RobA_TF
+            HMM Removed:  NF028537.1      P_eth_NH2_trans
+            HMM Removed:  NF030466.0      TIGR02052
+            HMM Removed:  NF030467.0      TIGR02053
+            HMM Removed:  NF033086.2      penta_rpt_Qnr
+            HMM Removed:  NF033124.1      estX
+            HMM Removed:  NF033134.0      cmlA_floR
+            HMM Removed:  NF033138.1      RND-peri-MexC
+            HMM Removed:  NF033142.1      efflux_OM_AdeC
+            HMM Removed:  NF033143.1      efflux_OM_AdeK
+            HMM Removed:  NF033184.1      B3_Acin_new1
+            HMM Removed:  NF033480.1      bifunc_MprF
+            HMM Removed:  NF033553.1      MerP_Gpos
+            HMM Removed:  NF033555.1      lyase_MerB
+            HMM Removed:  NF033556.1      MerTP_fusion
+            HMM Removed:  NF033560.1      merT_RC607
+            HMM Removed:  NF033565.0      trans_MerF
+            HMM Removed:  NF033606.1      heat_AAA_ClpK
+            HMM Removed:  NF033607.0      disagg_AAA_ClpG
+            HMM Removed:  NF033617.1      RND_permease_2
+            HMM Removed:  NF033627.1      intimin_all
+            HMM Removed:  NF033636.1      acid_shock_Asr
+           HMM Modified:  NF033408.2 polymyxin_MCR3 updated to NF033408.5 polymyxin_MCR3
+         Family Removed:  -               cfrC
+           Family Added:  -               cfr(B)
+           Family Added:  -               cfr(C)
+           Family Added:  -               cfr-Cb
+         Family Changed:  NF033408.2 mcr-3 updated to NF033408.5 mcr-3
+
+---------------------------------------------------------------------
+Changes included in 2018-05-15.1
+---------------------------------------------------------------------
+- Data Changes:
+        Protein Removed:  WP_010886396.1  lmr(B)
+              HMM Added:  NF033614.1      APH_6_Ic_gen
+              HMM Added:  NF033617.1      RND_permease_2
+              HMM Added:  NF033626.1      blaBKC_GPC
+              HMM Added:  NF033627.1      intimin_all
+              HMM Added:  NF033636.1      acid_shock_Asr
+           HMM Modified:  NF000011.1      APH_6_Ic updated to NF000011.2 APH_6_Ic
+           HMM Modified:  NF000221.3      FosA updated to NF000221.4 FosA
+           HMM Modified:  NF000282.1      RND_permease_1 updated to NF000282.2 RND_permease_1
+           HMM Modified:  NF000428.2      blaFRI updated to NF000428.4 blaFRI
+           HMM Modified:  NF033582.0      blaALI updated to NF033582.2 blaALI
+         Family Removed:  NF000060.1      lmr(B)
+           Family Added:  NF033626.1      blaBKC_GPC
+           Family Added:  -               blaGPC
+- Algorithm Changes:
+    - Partial proteins identified as "Method" PARTIAL if length of blast
+      alignment > 50% and < 90% of database protein.
+
+---------------------------------------------------------------------
+Changes included in 2018-05-08.1  RELEASE CANDIDATE
+---------------------------------------------------------------------
+- Addition of handling for genbank plasmid gff
+
+---------------------------------------------------------------------
+Changes included in 2018-04-16.1
+---------------------------------------------------------------------
+- Addition of file format checking for FASTA and GFF files before AMRFinder blast and HMM searches are run
+- Altered format of fam.tab file to include NF accessions for families
+- Removal of non-reportable families from fam.tab

data/amrfinder/database_format_version.txt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/database_format_version.txt

data/amrfinder/database_format_version.txt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/database_format_version.txt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,1 @@
+3.6.1

data/amrfinder/fam.tab

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/fam.tab

data/amrfinder/fam.tab

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/fam.tab Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,1530 @@
+#fam_id parent_fam_id gene_symbol hmm_id hmm_tc1 hmm_tc2 blastrule_complete_ident blastrule_complete_wp_coverage blastrule_complete_br_coverage blastrule_partial_ident blastrule_partial_wp_coverage blastrule_partial_br_coverage reportable type subtype class subclass family_name
+1567214_ble ble ble NF000028.1 250.00 250.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR BLEOMYCIN BLEOMYCIN BLMA family bleomycin binding protein
+ACID STRESS - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 STRESS ACID
+ALL - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0
+AME AMR - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 AMR AMR aminoglycoside modifying enzymes
+AMR ALL - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 AMR AMR
+ANTIGEN VIRULENCE - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 VIRULENCE ANTIGEN
+BIOCIDE STRESS - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 STRESS BIOCIDE
+BcII bla-B1 bla2 NF033095.1 500.00 500.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR BETA-LACTAM CARBAPENEM BcII family subclass B1 metallo-beta-lactamase
+CDF_efflux METAL - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 STRESS METAL CDF family cation efflux transporter
+CMY2-MIR-ACT-EC bla-C ampC NF012173.1 680.00 680.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR BETA-LACTAM BETA-LACTAM CMY2/MIR/ACT/EC family class C beta-lactamase
+EFFLUX AMR - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 AMR AMR efflux
+HARLDQ_not_B3 bla-B3 - NF000405.1 350.00 350.00 0.00 0.00 0.00 0.00 0.00 0.00 0 AMR AMR HARLDQ motif MBL-fold protein
+HEAT STRESS xxx - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 STRESS HEAT
+HTH_5 METAL - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 STRESS METAL ArsR/SmtB family metalloregulatory transcriptional repressor
+LHR_hdeD HEAT hdeD-GI - 0.00 0.00 90.00 90.00 90.00 93.00 90.00 25.00 1 STRESS HEAT heat resistance membrane protein HdeD-GI
+LHR_hsp20A HEAT hsp20 - 0.00 0.00 94.00 90.00 90.00 96.00 90.00 25.00 1 STRESS HEAT small heat shock protein sHSP20
+LHR_hsp20B HEAT shsP - 0.00 0.00 93.00 90.00 90.00 94.00 90.00 25.00 1 STRESS HEAT small heat shock protein sHSP20-GI
+LHR_kefB HEAT kefB-GI - 0.00 0.00 86.00 90.00 90.00 90.00 90.00 25.00 1 STRESS HEAT heat resistance system K+/H+ antiporter KefB-GI
+LHR_psiE HEAT psi-GI - 0.00 0.00 88.00 90.00 90.00 90.00 90.00 25.00 1 STRESS HEAT heat resistance protein PsiE-GI
+LHR_trx HEAT trxLHR - 0.00 0.00 85.00 90.00 90.00 90.00 90.00 25.00 1 STRESS HEAT heat resistance system thioredoxin Trx-GI
+LHR_yfdX1 HEAT yfdX1 - 0.00 0.00 88.00 90.00 90.00 90.00 90.00 25.00 1 STRESS HEAT heat resistance protein YfdX1
+LHR_yfdX2 HEAT yfdX2 - 0.00 0.00 90.00 90.00 90.00 90.00 90.00 25.00 1 STRESS HEAT heat resistance protein YfdX2
+MATE_efflux EFFLUX - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 AMR AMR multidrug efflux MATE transporter
+METAL-RND-IM METAL xxx - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 STRESS METAL cation efflux RND transporter permease subunit
+METAL STRESS xxx - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 STRESS METAL Metal Resistance
+MFS_efflux_CHL MFS_efflux cml - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR PHENICOL CHLORAMPHENICOL chloramphenicol efflux MFS transporter
+MFS_efflux_qac BIOCIDE qac NF000089.1 900.00 900.00 0.00 0.00 0.00 0.00 0.00 0.00 2 STRESS BIOCIDE QUATERNARY AMMONIUM QUATERNARY AMMONIUM QacA/B family quaternary ammonium compound efflux MFS transporter
+MFS_efflux EFFLUX - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 AMR AMR multidrug efflux MFS transporter
+MerP_Gneg merP merP TIGR02052.1 92.55 92.55 0.00 0.00 0.00 0.00 0.00 0.00 1 STRESS METAL MERCURY MERCURY mercury resistance system periplasmic binding protein MerP
+OM_sidero VIRULENCE_E._coli sidero - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 VIRULENCE VIRULENCE TonB-dependent siderophore receptor
+P-type_ATPase METAL - - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 STRESS..ransferase Vat(A)
+vat(B) vat vat(B) - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin A O-acetyltransferase Vat(B)
+vat(C) vat vat(C) NF000097.1 425.00 425.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin A O-acetyltransferase Vat(C)
+vat(D) vat vat(D) NF000111.1 400.00 400.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin A O-acetyltransferase Vat(D)
+vat(E) vat vat(E) NF000020.1 450.00 450.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin A O-acetyltransferase Vat(E)
+vat(F) vat vat(F) NF000147.1 400.00 400.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin A O-acetyltransferase Vat(F)
+vat(H) vat vat(H) NF000504.1 475.00 425.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin A O-acetyltransferase Vat(H)
+vat(I) vat vatI NF033468.1 415.00 415.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin A O-acetyltransferase Vat(I)
+vat AMR vat NF000311.1 300.00 300.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN Vat family streptogramin A O-acetyltransferase
+vga(A) vga vga(A) - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR LINCOSAMIDE LINCOSAMIDE ABC-F type ribosomal protection protein Vga(A)
+vga(B) vga vga(B) - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR LINCOSAMIDE LINCOSAMIDE ABC-F type ribosomal protection protein Vga(B)
+vga(C) vga vga(C) - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR LINCOSAMIDE LINCOSAMIDE ABC-F type ribosomal protection protein Vga(C)
+vga(D) vga vga(D) - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR LINCOSAMIDE LINCOSAMIDE ABC-F type ribosomal protection protein Vga(D)
+vga(E) vga vga(E) - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR LINCOSAMIDE LINCOSAMIDE ABC-F type ribosomal protection protein Vga(E)
+vga abc-f vga NF000170.1 800.00 800.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR LINCOSAMIDE LINCOSAMIDE Vga family ABC-F type ribosomal protection protein
+vgb(A) vgb vgb(A) NF000022.1 600.00 600.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin B lyase Vgb(A)
+vgb(B) vgb vgb(B) NF000096.1 600.00 600.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin B lyase Vgb(B)
+vgb(C) vgb vgbC - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin B lyase Vgb(C)
+vgb AMR vgb - 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR STREPTOGRAMIN STREPTOGRAMIN streptogramin B lyase
+virF VIRULENCE_E._coli virF - 0.00 0.00 94.00 90.00 90.00 96.00 90.00 25.00 1 VIRULENCE VIRULENCE AraC family invasion system transcriptional regulator VirF
+vmlR abc-f vmlR - 0.00 0.00 90.00 90.00 90.00 96.00 90.00 25.00 2 AMR AMR MACROLIDE/PLEUROMUTILIN LINCOSAMIDE/STREPTOGRAMIN/TIAMULIN ABC-F type ribosomal protection protein VmlR
+vph AMR vph NF000088.1 400.00 400.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR TUBERACTINOMYCIN VIOMYCIN viomycin phosphotransferase
+ybtP VIRULENCE ybtP - 0.00 0.00 85.00 90.00 90.00 96.00 90.00 25.00 1 VIRULENCE VIRULENCE yersiniabactin ABC transporter ATP-binding/permease protein YbtP
+ybtQ VIRULENCE ybtQ - 0.00 0.00 85.00 90.00 90.00 96.00 90.00 25.00 1 VIRULENCE VIRULENCE yersiniabactin ABC transporter ATP-binding/permease protein YbtQ
+yfeA VIRULENCE yfeA - 0.00 0.00 83.00 90.00 90.00 88.00 90.00 25.00 1 VIRULENCE VIRULENCE iron/manganese ABC transporter substrate-binding protein YfeA
+yfeB VIRULENCE yfeB - 0.00 0.00 86.00 90.00 90.00 96.00 90.00 25.00 1 VIRULENCE VIRULENCE iron/manganese ABC transporter ATP-binding protein YfeB
+yfeD VIRULENCE yfeD - 0.00 0.00 88.00 90.00 90.00 92.00 90.00 25.00 1 VIRULENCE VIRULENCE iron/manganese ABC transporter permease subunit YfeD
+zbmA ble zbmA NF000479.1 280.00 280.00 0.00 0.00 0.00 0.00 0.00 0.00 2 AMR AMR BLEOMYCIN ZORBAMYCIN zorbamycin binding protein ZbmA

data/amrfinder/taxgroup.tab

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/taxgroup.tab

data/amrfinder/taxgroup.tab

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/taxgroup.tab Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,9 @@
+#taxgroup gpipe_taxgroup number_of_nucl_ref_genes
+Campylobacter Campylobacter 2
+Enterococcus_faecalis Enterococcus_faecalis 0
+Enterococcus_faecium Enterococcus_faecium 0
+Escherichia Escherichia_coli_Shigella 5
+Klebsiella Klebsiella 0
+Salmonella Salmonella 1
+Staphylococcus Staphylococcus_pseudintermedius 0
+Vibrio_cholerae Vibrio_cholerae 0

data/amrfinder/version.txt

diff -r 000000000000 -r 8be2feb96994 data/amrfinder/version.txt

data/amrfinder/version.txt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/amrfinder/version.txt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,1 @@
+2020-01-06.1

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_2018-10-09.jld

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_2018-10-09.jld

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_2018-10-09.jld

Binary file data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_2018-10-09.jld has changed

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_2018-10-09.jld

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_2018-10-09.jld.profile

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_2018-10-09.jld

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_2018-10-09.jld.profile Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,6988 @@
+ST adk fumC gyrB icd mdh purA recA clonal_complex
+1 4 2 2 4 4 4 4
+2 5 3 2 6 5 5 4
+3 6 4 3 7 7 7 6 ST20 Cplx
+4 6 5 4 8 8 8 2 ST10 Cplx
+5 7 6 5 9 9 8 2 ST13 Cplx
+6 8 7 1 1 10 8 6
+7 9 8 5 1 11 8 7
+8 10 9 5 10 12 9 2 ST165 Cplx
+9 6 4 3 7 7 7 8 ST20 Cplx
+10 10 11 4 8 8 8 2 ST10 Cplx
+11 12 12 8 12 15 2 2 ST11 Cplx
+12 13 13 9 13 16 10 9 ST12 Cplx
+13 6 6 5 9 9 8 2 ST13 Cplx
+14 14 14 10 14 17 7 10 ST14 Cplx
+15 15 15 11 15 18 11 11
+16 6 4 12 16 9 7 12 ST29 Cplx
+17 6 4 3 17 7 7 6 ST20 Cplx
+18 14 14 10 14 19 7 10 ST14 Cplx
+19 15 16 10 15 18 12 11
+20 6 4 3 18 7 7 6 ST20 Cplx
+21 16 4 12 16 9 7 7 ST29 Cplx
+22 6 17 7 19 1 2 2 ST280 Cplx
+23 6 4 12 1 20 13 7 ST23 Cplx
+24 17 18 13 20 18 14 13
+25 6 6 14 21 9 7 7
+26 6 19 15 18 11 8 14
+27 16 20 12 16 9 7 7 ST29 Cplx
+28 13 21 13 22 17 14 15 ST28 Cplx
+29 6 4 12 16 9 7 7 ST29 Cplx
+30 18 22 16 23 5 15 4
+31 18 22 17 6 5 5 4 ST31 Cplx
+32 19 23 18 24 21 2 16 ST32 Cplx
+33 6 4 4 1 22 8 7
+34 10 11 4 1 8 8 2 ST10 Cplx
+35 20 24 19 13 23 16 17
+37 21 22 20 6 5 17 18
+38 4 26 2 25 5 5 19 ST38 Cplx
+39 22 4 21 10 24 18 7
+40 6 4 5 26 20 8 14 ST40 Cplx
+41 10 27 5 8 25 7 2 ST226 Cplx
+42 23 28 22 27 5 16 4
+43 24 11 4 8 8 8 2 ST10 Cplx
+44 10 11 4 8 8 8 7 ST10 Cplx
+45 6 7 23 1 8 8 2
+46 8 7 1 8 8 8 6 ST46 Cplx
+47 8 11 5 1 7 18 6
+48 6 11 4 8 8 8 2 ST10 Cplx
+49 25 11 4 8 8 8 2 ST10 Cplx
+50 26 7 4 1 8 8 6
+51 6 4 1 13 17 8 20
+52 6 11 5 1 20 8 2
+53 9 29 12 1 11 13 6
+54 6 30 5 1 24 8 21
+55 6 4 4 18 20 8 14 ST155 Cplx
+56 6 4 4 18 24 5 14 ST155 Cplx
+57 6 31 5 28 1 1 2 ST350 Cplx
+58 6 4 4 16 24 8 14 ST155 Cplx
+59 27 32 24 29 26 19 22 ST59 Cplx
+60 28 33 24 29 26 20 2
+61 29 12 8 12 15 2 23 ST11 Cplx
+62 28 33 25 29 7 11 24
+63 30 11 5 8 7 21 2
+64 31 34 26 30 27 22 17
+65 28 33 25 29 1 11 2
+66 6 22 20 6 5 5 2
+67 6 19 5 1 9 8 7
+68 33 26 2 31 5 16 19
+69 21 35 27 6 5 5 4 ST69 Cplx
+70 34 36 28 25 28 16 4
+71 34 37 28 25 4 16 4
+72 35 37 29 25 4 5 18 ST405 Cplx
+73 36 24 9 13 17 11 25 ST73 Cplx
+74 36 24 9 13 17 5 25 ST73 Cplx
+75 6 6 5 10 20 23 6
+76 13 13 9 13 17 10 26
+77 6 7 5 1 8 18 27 ST206 Cplx
+78 37 38 19 32 17 24 26
+79 37 38 19 32 17 7 26
+80 13 24 19 14 23 1 10 ST568 Cplx
+81 14 14 10 14 17 7 21 ST14 Cplx
+82 38 39 30 13 29 25 28
+83 13 38 19 13 30 25 29
+84 6 29 31 16 24 8 2
+85 6 6 32 26 11 26 7
+86 9 6 33 33 24 8 7 ST86 Cplx
+87 6 11 14 8 20 8 2
+88 6 4 12 1 20 12 7 ST23 Cplx
+89 39 7 4 34 20 7 7
+90 6 4 12 1 20 8 7 ST23 Cplx
+91 13 40 34 13 23 28 30
+92 40 14 19 36 23 11 10
+93 6 11 4 10 7 8 6 ST168 Cplx
+94 41 6 5 16 11 8 7 ST448 Cplx
+95 37 38 19 37 17 11 26 ST95 Cplx
+96 10 11 5 38 7 8 2
+97 42 4 12 16 9 7 12 ST29 Cplx
+98 10 11 4 39 8 8 2 ST10 Cplx
+99 6 4 22 18 9 26 7
+100 10 27 5 10 12 9 2 ST165 Cplx
+101 43 41 15 18 11 7 6 ST101 Cplx
+102 44 42 35 40 32 29 31
+103 45 4 36 10 24 18 32
+104 13 24 9 13 17 11 25 ST73 Cplx
+105 13 43 19 36 17 10 10
+106 21 35 27 6 5 8 4 ST69 Cplx
+107 13 21 19 22 17 14 15 ST28 Cplx
+108 46 36 37 25 5 16 33
+109 6 6 1 16 9 13 2
+110 47 40 19 13 17 25 30
+111 6 29 14 16 24 8 2
+112 13 44 9 22 16 30 34
+113 16 4 38 16 9 7 7 ST29 Cplx
+114 4 2 2 41 4 4 4
+115 4 26 39 25 5 31 19
+116 8 11 40 42 7 18 6
+117 20 45 41 43 5 32 2
+118 31 4 42 44 15 33 17
+119 48 46 43 45 11 34 35
+120 49 4 44 9 11 35 7
+121 13 21 13 22 17 36 15 ST28 Cplx
+122 15 24 10 46 33 37 36 ST122 Cplx
+123 50 47 19 37 17 30 2
+124 6 19 3 18 9 38 6
+125 51 48 45 47 34 39 37
+126 13 43 19 37 17 25 25
+127 13 14 19 36 23 11 10
+128 52 49 46 48 35 40 38
+129 6 23 3 26 9 7 7
+130 18 22 20 6 5 5 4 ST31 Cplx
+131 53 40 47 13 36 28 29 ST131 Cplx
+132 35 50 22 49 37 41 39
+133 51 48 48 50 34 42 37
+134 13 44 49 13 16 10 34
+135 13 39 50 13 16 37 25
+136 38 39 30 13 17 11 28
+137 19 23 51 24 21 2 16 ST3..
+7284 683 26 39 25 5 31 19
+7285 6 4 14 788 20 62 7
+7286 684 7 4 8 8 8 2
+7287 10 11 4 8 8 555 2
+7288 9 1002 33 131 24 8 7
+7289 6 23 32 789 627 8 7
+7290 10 11 4 790 8 8 2
+7291 10 23 4 1 8 8 6
+7292 618 4 4 16 24 8 14
+7293 10 7 4 8 12 116 525
+7294 10 1003 4 8 8 8 7
+7295 76 1004 19 37 30 1 25
+7296 4 26 621 25 5 5 19
+7297 83 260 155 45 1 1 2
+7298 503 4 12 791 20 13 7
+7299 10 11 622 8 8 8 2
+7300 6 95 623 1 9 8 6
+7301 10 11 4 8 8 8 323
+7302 64 4 96 792 24 8 6
+7303 6 23 15 88 9 8 7
+7304 10 11 4 463 8 13 73
+7305 10 11 4 8 8 556 2
+7306 6 1005 5 16 11 8 7
+7307 83 608 155 793 1 1 17
+7308 10 1006 4 8 8 8 2
+7309 6 5 4 8 628 8 2
+7310 6 4 12 1 20 12 526
+7311 6 4 12 16 629 7 7
+7312 6 4 3 794 11 8 6
+7313 64 7 1 1 614 8 6
+7314 6 11 4 249 8 8 2
+7315 136 11 4 1 9 18 7
+7316 48 46 43 45 11 557 35
+7317 10 11 5 12 8 18 2
+7318 685 11 4 8 8 8 2
+7319 10 11 4 8 630 8 2
+7320 129 354 624 13 30 14 13
+7321 10 11 4 8 8 8 527
+7322 6 1007 14 16 24 8 14
+7323 10 11 4 795 8 8 405
+7324 6 95 3 18 9 558 6
+7325 54 22 4 342 40 16 4
+7326 6 133 12 1 9 5 7
+7327 686 11 4 8 8 8 133
+7328 35 132 2 796 37 5 4
+7329 6 4 14 16 358 8 14
+7330 687 103 19 36 23 44 26
+7331 10 11 4 8 631 8 2
+7332 6 1008 362 52 632 50 528
+7333 688 4 12 1 20 13 7
+7334 689 11 4 8 8 13 73
+7335 6 4 4 797 43 8 6
+7336 6 4 7 45 11 239 7
+7337 10 11 4 8 633 8 2
+7338 136 1009 5 1 8 18 2
+7339 27 32 24 29 26 9 22
+7340 13 40 19 13 23 559 109
+7341 238 52 10 13 17 25 17
+7342 20 45 41 798 5 32 2
+7343 8 7 625 8 8 8 6
+7344 76 43 19 14 18 68 529
+7345 51 48 328 374 34 42 37
+7346 690 43 9 37 17 37 25
+7347 484 48 467 266 34 42 37
+7348 51 649 220 47 235 42 37
+7349 691 48 220 799 235 42 37
+7350 51 48 220 266 235 42 37
+7351 488 1010 470 800 448 414 530
+7352 10 11 4 12 8 45 67
+7353 6 11 4 10 7 560 6
+7354 6 1011 4 801 634 8 6
+7355 6 1011 4 802 634 8 6
+7356 6 1011 4 802 635 8 6
+7357 6 1011 4 802 634 241 6
+7358 692 37 29 25 4 5 73
+7359 6 402 14 16 358 2 14
+7360 6 11 626 803 7 8 6
+7361 6 4 12 18 24 8 6
+7362 693 1012 193 804 636 561 142
+7363 68 80 627 45 7 54 7
+7364 694 4 1 5 1 1 5
+7365 695 111 85 483 109 149 75
+7366 112 11 5 12 8 7 86
+7367 6 685 4 8 8 8 2
+7368 10 11 4 8 8 8 81
+7369 10 11 4 805 8 8 2
+7370 6 11 4 8 637 8 2
+7371 1 988 1 5 1 1 51
+7372 11 63 628 1 14 7 7
+7373 11 63 7 552 14 7 7
+7374 67 77 629 69 5 1 59
+7375 1 4 1 735 1 1 1
+7376 10 11 4 8 8 8 531
+7377 207 389 260 254 301 554 2
+7378 1 4 1 806 1 1 5
+7379 1 4 1 5 1 562 51
+7380 1 1013 1 5 6 1 5
+7381 1 4 1 807 1 1 5
+7382 501 23 630 808 329 309 2
+7383 696 4 1 5 1 1 5
+7384 6 61 6 11 13 563 50
+7385 1 10 1 1 1 1 532
+7386 6 11 4 8 80 8 2
+7387 6 27 159 10 112 1 2
+7388 13 14 19 36 638 11 10
+7389 13 14 631 36 23 11 10
+7390 697 14 19 36 23 11 10
+7391 13 40 93 13 23 28 122
+7392 53 40 632 13 36 28 29
+7393 53 1015 47 13 36 28 29
+7394 6 23 3 18 9 7 7
+7395 35 37 29 25 4 564 73
+7396 53 40 633 13 36 28 29
+7397 358 1016 15 16 9 8 7
+7398 16 4 634 16 9 7 7
+7399 53 40 635 13 36 28 29
+7400 6 4 33 16 11 7 14
+7401 21 35 27 6 5 565 4
+7402 10 374 5 10 8 8 2
+7403 698 1017 380 320 268 17 286
+7404 603 4 33 16 11 8 6
+7405 457 6 33 131 24 8 7
+7406 603 4 12 1 20 18 7
+7407 8 7 1 8 125 211 6
+7408 603 4 12 1 20 12 7
+7409 383 23 109 8 8 8 2
+7410 429 19 33 26 11 8 6
+7411 10 11 478 8 8 250 2
+7412 429 556 32 317 43 1 2
+7413 19 23 636 24 21 2 16
+7414 163 1018 85 189 280 275 75
+7415 163 393 637 809 68 246 75
+7416 51 48 220 47 34 277 37
+7417 16 4 12 16 639 7 7
+7418 6 4 127 810 24 8 6
+7419 11 1019 7 1 14 7 7
+7420 6 4 33 132 20 8 7
+7421 76 24 13 811 23 76 79
+7422 36 1020 9 13 17 11 25
+7423 12 1021 8 12 15 2 2
+7424 10 553 4 1 8 8 2
+7425 290 54 4 324 35 40 223
+7426 21 35 27 748 5 5 4
+7427 6 2 519 627 180 16 433
+7428 9 19 15 18 9 8 6
+7429 92 4 638 96 70 58 2
+7430 92 4 87 812 70 58 2
+7431 12 12 639 12 15 2 2
+7432 699 4 3 17 7 7 6

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld

Binary file data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld has changed

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld.profile

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_k31_m023_2018-10-09.jld.profile Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,6988 @@
+ST adk fumC gyrB icd mdh purA recA clonal_complex
+1 4 2 2 4 4 4 4
+2 5 3 2 6 5 5 4
+3 6 4 3 7 7 7 6 ST20 Cplx
+4 6 5 4 8 8 8 2 ST10 Cplx
+5 7 6 5 9 9 8 2 ST13 Cplx
+6 8 7 1 1 10 8 6
+7 9 8 5 1 11 8 7
+8 10 9 5 10 12 9 2 ST165 Cplx
+9 6 4 3 7 7 7 8 ST20 Cplx
+10 10 11 4 8 8 8 2 ST10 Cplx
+11 12 12 8 12 15 2 2 ST11 Cplx
+12 13 13 9 13 16 10 9 ST12 Cplx
+13 6 6 5 9 9 8 2 ST13 Cplx
+14 14 14 10 14 17 7 10 ST14 Cplx
+15 15 15 11 15 18 11 11
+16 6 4 12 16 9 7 12 ST29 Cplx
+17 6 4 3 17 7 7 6 ST20 Cplx
+18 14 14 10 14 19 7 10 ST14 Cplx
+19 15 16 10 15 18 12 11
+20 6 4 3 18 7 7 6 ST20 Cplx
+21 16 4 12 16 9 7 7 ST29 Cplx
+22 6 17 7 19 1 2 2 ST280 Cplx
+23 6 4 12 1 20 13 7 ST23 Cplx
+24 17 18 13 20 18 14 13
+25 6 6 14 21 9 7 7
+26 6 19 15 18 11 8 14
+27 16 20 12 16 9 7 7 ST29 Cplx
+28 13 21 13 22 17 14 15 ST28 Cplx
+29 6 4 12 16 9 7 7 ST29 Cplx
+30 18 22 16 23 5 15 4
+31 18 22 17 6 5 5 4 ST31 Cplx
+32 19 23 18 24 21 2 16 ST32 Cplx
+33 6 4 4 1 22 8 7
+34 10 11 4 1 8 8 2 ST10 Cplx
+35 20 24 19 13 23 16 17
+37 21 22 20 6 5 17 18
+38 4 26 2 25 5 5 19 ST38 Cplx
+39 22 4 21 10 24 18 7
+40 6 4 5 26 20 8 14 ST40 Cplx
+41 10 27 5 8 25 7 2 ST226 Cplx
+42 23 28 22 27 5 16 4
+43 24 11 4 8 8 8 2 ST10 Cplx
+44 10 11 4 8 8 8 7 ST10 Cplx
+45 6 7 23 1 8 8 2
+46 8 7 1 8 8 8 6 ST46 Cplx
+47 8 11 5 1 7 18 6
+48 6 11 4 8 8 8 2 ST10 Cplx
+49 25 11 4 8 8 8 2 ST10 Cplx
+50 26 7 4 1 8 8 6
+51 6 4 1 13 17 8 20
+52 6 11 5 1 20 8 2
+53 9 29 12 1 11 13 6
+54 6 30 5 1 24 8 21
+55 6 4 4 18 20 8 14 ST155 Cplx
+56 6 4 4 18 24 5 14 ST155 Cplx
+57 6 31 5 28 1 1 2 ST350 Cplx
+58 6 4 4 16 24 8 14 ST155 Cplx
+59 27 32 24 29 26 19 22 ST59 Cplx
+60 28 33 24 29 26 20 2
+61 29 12 8 12 15 2 23 ST11 Cplx
+62 28 33 25 29 7 11 24
+63 30 11 5 8 7 21 2
+64 31 34 26 30 27 22 17
+65 28 33 25 29 1 11 2
+66 6 22 20 6 5 5 2
+67 6 19 5 1 9 8 7
+68 33 26 2 31 5 16 19
+69 21 35 27 6 5 5 4 ST69 Cplx
+70 34 36 28 25 28 16 4
+71 34 37 28 25 4 16 4
+72 35 37 29 25 4 5 18 ST405 Cplx
+73 36 24 9 13 17 11 25 ST73 Cplx
+74 36 24 9 13 17 5 25 ST73 Cplx
+75 6 6 5 10 20 23 6
+76 13 13 9 13 17 10 26
+77 6 7 5 1 8 18 27 ST206 Cplx
+78 37 38 19 32 17 24 26
+79 37 38 19 32 17 7 26
+80 13 24 19 14 23 1 10 ST568 Cplx
+81 14 14 10 14 17 7 21 ST14 Cplx
+82 38 39 30 13 29 25 28
+83 13 38 19 13 30 25 29
+84 6 29 31 16 24 8 2
+85 6 6 32 26 11 26 7
+86 9 6 33 33 24 8 7 ST86 Cplx
+87 6 11 14 8 20 8 2
+88 6 4 12 1 20 12 7 ST23 Cplx
+89 39 7 4 34 20 7 7
+90 6 4 12 1 20 8 7 ST23 Cplx
+91 13 40 34 13 23 28 30
+92 40 14 19 36 23 11 10
+93 6 11 4 10 7 8 6 ST168 Cplx
+94 41 6 5 16 11 8 7 ST448 Cplx
+95 37 38 19 37 17 11 26 ST95 Cplx
+96 10 11 5 38 7 8 2
+97 42 4 12 16 9 7 12 ST29 Cplx
+98 10 11 4 39 8 8 2 ST10 Cplx
+99 6 4 22 18 9 26 7
+100 10 27 5 10 12 9 2 ST165 Cplx
+101 43 41 15 18 11 7 6 ST101 Cplx
+102 44 42 35 40 32 29 31
+103 45 4 36 10 24 18 32
+104 13 24 9 13 17 11 25 ST73 Cplx
+105 13 43 19 36 17 10 10
+106 21 35 27 6 5 8 4 ST69 Cplx
+107 13 21 19 22 17 14 15 ST28 Cplx
+108 46 36 37 25 5 16 33
+109 6 6 1 16 9 13 2
+110 47 40 19 13 17 25 30
+111 6 29 14 16 24 8 2
+112 13 44 9 22 16 30 34
+113 16 4 38 16 9 7 7 ST29 Cplx
+114 4 2 2 41 4 4 4
+115 4 26 39 25 5 31 19
+116 8 11 40 42 7 18 6
+117 20 45 41 43 5 32 2
+118 31 4 42 44 15 33 17
+119 48 46 43 45 11 34 35
+120 49 4 44 9 11 35 7
+121 13 21 13 22 17 36 15 ST28 Cplx
+122 15 24 10 46 33 37 36 ST122 Cplx
+123 50 47 19 37 17 30 2
+124 6 19 3 18 9 38 6
+125 51 48 45 47 34 39 37
+126 13 43 19 37 17 25 25
+127 13 14 19 36 23 11 10
+128 52 49 46 48 35 40 38
+129 6 23 3 26 9 7 7
+130 18 22 20 6 5 5 4 ST31 Cplx
+131 53 40 47 13 36 28 29 ST131 Cplx
+132 35 50 22 49 37 41 39
+133 51 48 48 50 34 42 37
+134 13 44 49 13 16 10 34
+135 13 39 50 13 16 37 25
+136 38 39 30 13 17 11 28
+137 19 23 51 24 21 2 1..
+7284 683 26 39 25 5 31 19
+7285 6 4 14 788 20 62 7
+7286 684 7 4 8 8 8 2
+7287 10 11 4 8 8 555 2
+7288 9 1002 33 131 24 8 7
+7289 6 23 32 789 627 8 7
+7290 10 11 4 790 8 8 2
+7291 10 23 4 1 8 8 6
+7292 618 4 4 16 24 8 14
+7293 10 7 4 8 12 116 525
+7294 10 1003 4 8 8 8 7
+7295 76 1004 19 37 30 1 25
+7296 4 26 621 25 5 5 19
+7297 83 260 155 45 1 1 2
+7298 503 4 12 791 20 13 7
+7299 10 11 622 8 8 8 2
+7300 6 95 623 1 9 8 6
+7301 10 11 4 8 8 8 323
+7302 64 4 96 792 24 8 6
+7303 6 23 15 88 9 8 7
+7304 10 11 4 463 8 13 73
+7305 10 11 4 8 8 556 2
+7306 6 1005 5 16 11 8 7
+7307 83 608 155 793 1 1 17
+7308 10 1006 4 8 8 8 2
+7309 6 5 4 8 628 8 2
+7310 6 4 12 1 20 12 526
+7311 6 4 12 16 629 7 7
+7312 6 4 3 794 11 8 6
+7313 64 7 1 1 614 8 6
+7314 6 11 4 249 8 8 2
+7315 136 11 4 1 9 18 7
+7316 48 46 43 45 11 557 35
+7317 10 11 5 12 8 18 2
+7318 685 11 4 8 8 8 2
+7319 10 11 4 8 630 8 2
+7320 129 354 624 13 30 14 13
+7321 10 11 4 8 8 8 527
+7322 6 1007 14 16 24 8 14
+7323 10 11 4 795 8 8 405
+7324 6 95 3 18 9 558 6
+7325 54 22 4 342 40 16 4
+7326 6 133 12 1 9 5 7
+7327 686 11 4 8 8 8 133
+7328 35 132 2 796 37 5 4
+7329 6 4 14 16 358 8 14
+7330 687 103 19 36 23 44 26
+7331 10 11 4 8 631 8 2
+7332 6 1008 362 52 632 50 528
+7333 688 4 12 1 20 13 7
+7334 689 11 4 8 8 13 73
+7335 6 4 4 797 43 8 6
+7336 6 4 7 45 11 239 7
+7337 10 11 4 8 633 8 2
+7338 136 1009 5 1 8 18 2
+7339 27 32 24 29 26 9 22
+7340 13 40 19 13 23 559 109
+7341 238 52 10 13 17 25 17
+7342 20 45 41 798 5 32 2
+7343 8 7 625 8 8 8 6
+7344 76 43 19 14 18 68 529
+7345 51 48 328 374 34 42 37
+7346 690 43 9 37 17 37 25
+7347 484 48 467 266 34 42 37
+7348 51 649 220 47 235 42 37
+7349 691 48 220 799 235 42 37
+7350 51 48 220 266 235 42 37
+7351 488 1010 470 800 448 414 530
+7352 10 11 4 12 8 45 67
+7353 6 11 4 10 7 560 6
+7354 6 1011 4 801 634 8 6
+7355 6 1011 4 802 634 8 6
+7356 6 1011 4 802 635 8 6
+7357 6 1011 4 802 634 241 6
+7358 692 37 29 25 4 5 73
+7359 6 402 14 16 358 2 14
+7360 6 11 626 803 7 8 6
+7361 6 4 12 18 24 8 6
+7362 693 1012 193 804 636 561 142
+7363 68 80 627 45 7 54 7
+7364 694 4 1 5 1 1 5
+7365 695 111 85 483 109 149 75
+7366 112 11 5 12 8 7 86
+7367 6 685 4 8 8 8 2
+7368 10 11 4 8 8 8 81
+7369 10 11 4 805 8 8 2
+7370 6 11 4 8 637 8 2
+7371 1 988 1 5 1 1 51
+7372 11 63 628 1 14 7 7
+7373 11 63 7 552 14 7 7
+7374 67 77 629 69 5 1 59
+7375 1 4 1 735 1 1 1
+7376 10 11 4 8 8 8 531
+7377 207 389 260 254 301 554 2
+7378 1 4 1 806 1 1 5
+7379 1 4 1 5 1 562 51
+7380 1 1013 1 5 6 1 5
+7381 1 4 1 807 1 1 5
+7382 501 23 630 808 329 309 2
+7383 696 4 1 5 1 1 5
+7384 6 61 6 11 13 563 50
+7385 1 10 1 1 1 1 532
+7386 6 11 4 8 80 8 2
+7387 6 27 159 10 112 1 2
+7388 13 14 19 36 638 11 10
+7389 13 14 631 36 23 11 10
+7390 697 14 19 36 23 11 10
+7391 13 40 93 13 23 28 122
+7392 53 40 632 13 36 28 29
+7393 53 1015 47 13 36 28 29
+7394 6 23 3 18 9 7 7
+7395 35 37 29 25 4 564 73
+7396 53 40 633 13 36 28 29
+7397 358 1016 15 16 9 8 7
+7398 16 4 634 16 9 7 7
+7399 53 40 635 13 36 28 29
+7400 6 4 33 16 11 7 14
+7401 21 35 27 6 5 565 4
+7402 10 374 5 10 8 8 2
+7403 698 1017 380 320 268 17 286
+7404 603 4 33 16 11 8 6
+7405 457 6 33 131 24 8 7
+7406 603 4 12 1 20 18 7
+7407 8 7 1 8 125 211 6
+7408 603 4 12 1 20 12 7
+7409 383 23 109 8 8 8 2
+7410 429 19 33 26 11 8 6
+7411 10 11 478 8 8 250 2
+7412 429 556 32 317 43 1 2
+7413 19 23 636 24 21 2 16
+7414 163 1018 85 189 280 275 75
+7415 163 393 637 809 68 246 75
+7416 51 48 220 47 34 277 37
+7417 16 4 12 16 639 7 7
+7418 6 4 127 810 24 8 6
+7419 11 1019 7 1 14 7 7
+7420 6 4 33 132 20 8 7
+7421 76 24 13 811 23 76 79
+7422 36 1020 9 13 17 11 25
+7423 12 1021 8 12 15 2 2
+7424 10 553 4 1 8 8 2
+7425 290 54 4 324 35 40 223
+7426 21 35 27 748 5 5 4
+7427 6 2 519 627 180 16 433
+7428 9 19 15 18 9 8 6
+7429 92 4 638 96 70 58 2
+7430 92 4 87 812 70 58 2
+7431 12 12 639 12 15 2 2
+7432 699 4 3 17 7 7 6

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/adk.tfa

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/adk.tfa

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/adk.tfa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/adk.tfa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,6720 @@
+>adk_1
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATTGTTGATCGTATCGTAGGCCGCCGCGTTCATGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACTGCACCGCTGATCGGCTACTACTCCAAAGAAGCGGAAGCGGGTA
+>adk_2
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTTACCGACGAACTGGTGATCGCGCTGGTTAAAGGGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATCGTTGACCGTATCGTCGGTCGCCGCGTTCACGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGTAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACAGCACCGCTGATCGGCTACTACTCCAAAGAAGCTGAAGCGGGTA
+>adk_3
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATTGTTGATCGTATCGTAGGCCGCCGCGTTCATGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTGCGTAAACGTCTGGTTGAATA
+CCATCAGATGACTGCACCGTTGATCGGCTACTACTCCAAAGAAGCGGAAGCGGGTA
+>adk_4
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTTACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATCGTTGACCGTATTGTCGGTCGCCGCGTTCACGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAACCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACTGCACCGCTGATCGGCTACTACTCCAAAGAAGCGGAAGCGGGTA
+>adk_5
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAATTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATCGTTGACCGTATCGTCGGTCGCCGCGTTCACGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACTGCACCGCTGATCGGCTACTACTCCAAAGAAGCGGAAGCGGGTA
+>adk_6
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATTGTTGATCGTATCGTAGGCCGCCGCGTTCATGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTGCGTAAACGTCTGGTTGAATA
+CCATCAGATGACTGCACCGCTGATCGGCTACTACTCCAAAGAAGCGGAAGCGGGTA
+>adk_7
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCACTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATTGTTGATCGTATCGTAGGCCGCCGCGTTCATGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGAC..GATGACAGCACCGCTGATCGGCTACTACTCCAAAGAAGCAGAAGCGGGTA
+>adk_820
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATCGTTGACCGTATCGTCGGTCGCCGCGTTCATGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTGAAGATGATCAGGAAGAGACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACAGCACCGCTGATCGGCTACTACTCCAAAGAAGCAGAAGCGGGTA
+>adk_821
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATCGTTGACCGTATCGTCGGTCGCCGCGTTCATGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAACTGACTGCCCGTAAAGATGATCAGGAAGAGACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACAGCACCGCTGATCGGCTACTACTCCAAAGAAGCAGAAGCGGGTA
+>adk_822
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATCGTTGACCGTATCGTCGGTCGCCGCGTTCATGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTAAAGATGATCAGGAAGAGACCGTACGTAAACGTCTGGTTGAATA
+CAATCAGATGACAGCACCGCTGATCGGCTACTACTCCAAAGAAGCAGAAGCGGGTA
+>adk_823
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCAGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGCAACGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATTGTTGACCGTATCGTAGGCCGCCGCGTTCATGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGTAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACTGCACCGCTGATCGGCTACTACTCCAAAGAAGCGGAAGCGGGTA
+>adk_824
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATGTGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGCAACGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCAATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATTGTTGACCGTATCGTAGGCCGCCGCGTTCACGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAGCTGACTACCCGTAAAGACGATCAGGAAGAGACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACTGCACCGCTGATCGGCTACTACTCCAAAGAAGCGGAAGCGGGTA
+>adk_825
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CCTTGCTCAGGAAGACTGCCGCAACGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCAATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATTGTTGACCGTATCGTAGGCCGCCGCGTTCACGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGA
+AGAGCTGACTACCCGTAAAGACGATCAGGAAGAGACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACTGCACCGCTGATCGGCTACTACTCCAAAGAAGCGGAAGCGGGTA
+>adk_826
+GGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATATGGTATTCCGCAAATCTCCAC
+TGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCG
+CATTGCTCAGGAAGACTGCCGTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCC
+GCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGATTACGTTCTGGAATTCGACGT
+ACCGGACGAACTGATTGTTGATCGTATCGTCGGTCGCCGCGTTCACGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGTAAAGACGACGTTACCGGTGA
+AGAACTGACTACCCGTAAAGACGATCAGGAAGAAACCGTACGTAAACGTCTGGTTGAATA
+CCATCAGATGACAGCACCGCTGATCGGCTACTACTCCAAAGAAGCGGAAGCGGGTA

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/ecoli.txt

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/ecoli.txt

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/ecoli.txt

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/ecoli.txt Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,6988 @@
+ST adk fumC gyrB icd mdh purA recA clonal_complex
+1 4 2 2 4 4 4 4
+2 5 3 2 6 5 5 4
+3 6 4 3 7 7 7 6 ST20 Cplx
+4 6 5 4 8 8 8 2 ST10 Cplx
+5 7 6 5 9 9 8 2 ST13 Cplx
+6 8 7 1 1 10 8 6
+7 9 8 5 1 11 8 7
+8 10 9 5 10 12 9 2 ST165 Cplx
+9 6 4 3 7 7 7 8 ST20 Cplx
+10 10 11 4 8 8 8 2 ST10 Cplx
+11 12 12 8 12 15 2 2 ST11 Cplx
+12 13 13 9 13 16 10 9 ST12 Cplx
+13 6 6 5 9 9 8 2 ST13 Cplx
+14 14 14 10 14 17 7 10 ST14 Cplx
+15 15 15 11 15 18 11 11
+16 6 4 12 16 9 7 12 ST29 Cplx
+17 6 4 3 17 7 7 6 ST20 Cplx
+18 14 14 10 14 19 7 10 ST14 Cplx
+19 15 16 10 15 18 12 11
+20 6 4 3 18 7 7 6 ST20 Cplx
+21 16 4 12 16 9 7 7 ST29 Cplx
+22 6 17 7 19 1 2 2 ST280 Cplx
+23 6 4 12 1 20 13 7 ST23 Cplx
+24 17 18 13 20 18 14 13
+25 6 6 14 21 9 7 7
+26 6 19 15 18 11 8 14
+27 16 20 12 16 9 7 7 ST29 Cplx
+28 13 21 13 22 17 14 15 ST28 Cplx
+29 6 4 12 16 9 7 7 ST29 Cplx
+30 18 22 16 23 5 15 4
+31 18 22 17 6 5 5 4 ST31 Cplx
+32 19 23 18 24 21 2 16 ST32 Cplx
+33 6 4 4 1 22 8 7
+34 10 11 4 1 8 8 2 ST10 Cplx
+35 20 24 19 13 23 16 17
+37 21 22 20 6 5 17 18
+38 4 26 2 25 5 5 19 ST38 Cplx
+39 22 4 21 10 24 18 7
+40 6 4 5 26 20 8 14 ST40 Cplx
+41 10 27 5 8 25 7 2 ST226 Cplx
+42 23 28 22 27 5 16 4
+43 24 11 4 8 8 8 2 ST10 Cplx
+44 10 11 4 8 8 8 7 ST10 Cplx
+45 6 7 23 1 8 8 2
+46 8 7 1 8 8 8 6 ST46 Cplx
+47 8 11 5 1 7 18 6
+48 6 11 4 8 8 8 2 ST10 Cplx
+49 25 11 4 8 8 8 2 ST10 Cplx
+50 26 7 4 1 8 8 6
+51 6 4 1 13 17 8 20
+52 6 11 5 1 20 8 2
+53 9 29 12 1 11 13 6
+54 6 30 5 1 24 8 21
+55 6 4 4 18 20 8 14 ST155 Cplx
+56 6 4 4 18 24 5 14 ST155 Cplx
+57 6 31 5 28 1 1 2 ST350 Cplx
+58 6 4 4 16 24 8 14 ST155 Cplx
+59 27 32 24 29 26 19 22 ST59 Cplx
+60 28 33 24 29 26 20 2
+61 29 12 8 12 15 2 23 ST11 Cplx
+62 28 33 25 29 7 11 24
+63 30 11 5 8 7 21 2
+64 31 34 26 30 27 22 17
+65 28 33 25 29 1 11 2
+66 6 22 20 6 5 5 2
+67 6 19 5 1 9 8 7
+68 33 26 2 31 5 16 19
+69 21 35 27 6 5 5 4 ST69 Cplx
+70 34 36 28 25 28 16 4
+71 34 37 28 25 4 16 4
+72 35 37 29 25 4 5 18 ST405 Cplx
+73 36 24 9 13 17 11 25 ST73 Cplx
+74 36 24 9 13 17 5 25 ST73 Cplx
+75 6 6 5 10 20 23 6
+76 13 13 9 13 17 10 26
+77 6 7 5 1 8 18 27 ST206 Cplx
+78 37 38 19 32 17 24 26
+79 37 38 19 32 17 7 26
+80 13 24 19 14 23 1 10 ST568 Cplx
+81 14 14 10 14 17 7 21 ST14 Cplx
+82 38 39 30 13 29 25 28
+83 13 38 19 13 30 25 29
+84 6 29 31 16 24 8 2
+85 6 6 32 26 11 26 7
+86 9 6 33 33 24 8 7 ST86 Cplx
+87 6 11 14 8 20 8 2
+88 6 4 12 1 20 12 7 ST23 Cplx
+89 39 7 4 34 20 7 7
+90 6 4 12 1 20 8 7 ST23 Cplx
+91 13 40 34 13 23 28 30
+92 40 14 19 36 23 11 10
+93 6 11 4 10 7 8 6 ST168 Cplx
+94 41 6 5 16 11 8 7 ST448 Cplx
+95 37 38 19 37 17 11 26 ST95 Cplx
+96 10 11 5 38 7 8 2
+97 42 4 12 16 9 7 12 ST29 Cplx
+98 10 11 4 39 8 8 2 ST10 Cplx
+99 6 4 22 18 9 26 7
+100 10 27 5 10 12 9 2 ST165 Cplx
+101 43 41 15 18 11 7 6 ST101 Cplx
+102 44 42 35 40 32 29 31
+103 45 4 36 10 24 18 32
+104 13 24 9 13 17 11 25 ST73 Cplx
+105 13 43 19 36 17 10 10
+106 21 35 27 6 5 8 4 ST69 Cplx
+107 13 21 19 22 17 14 15 ST28 Cplx
+108 46 36 37 25 5 16 33
+109 6 6 1 16 9 13 2
+110 47 40 19 13 17 25 30
+111 6 29 14 16 24 8 2
+112 13 44 9 22 16 30 34
+113 16 4 38 16 9 7 7 ST29 Cplx
+114 4 2 2 41 4 4 4
+115 4 26 39 25 5 31 19
+116 8 11 40 42 7 18 6
+117 20 45 41 43 5 32 2
+118 31 4 42 44 15 33 17
+119 48 46 43 45 11 34 35
+120 49 4 44 9 11 35 7
+121 13 21 13 22 17 36 15 ST28 Cplx
+122 15 24 10 46 33 37 36 ST122 Cplx
+123 50 47 19 37 17 30 2
+124 6 19 3 18 9 38 6
+125 51 48 45 47 34 39 37
+126 13 43 19 37 17 25 25
+127 13 14 19 36 23 11 10
+128 52 49 46 48 35 40 38
+129 6 23 3 26 9 7 7
+130 18 22 20 6 5 5 4 ST31 Cplx
+131 53 40 47 13 36 28 29 ST131 Cplx
+132 35 50 22 49 37 41 39
+133 51 48 48 50 34 42 37
+134 13 44 49 13 16 10 34
+135 13 39 50 13 16 37 25
+136 38 39 30 13 17 11 28
+137 19 23 51 24 21 2 16 ST..
+7284 683 26 39 25 5 31 19
+7285 6 4 14 788 20 62 7
+7286 684 7 4 8 8 8 2
+7287 10 11 4 8 8 555 2
+7288 9 1002 33 131 24 8 7
+7289 6 23 32 789 627 8 7
+7290 10 11 4 790 8 8 2
+7291 10 23 4 1 8 8 6
+7292 618 4 4 16 24 8 14
+7293 10 7 4 8 12 116 525
+7294 10 1003 4 8 8 8 7
+7295 76 1004 19 37 30 1 25
+7296 4 26 621 25 5 5 19
+7297 83 260 155 45 1 1 2
+7298 503 4 12 791 20 13 7
+7299 10 11 622 8 8 8 2
+7300 6 95 623 1 9 8 6
+7301 10 11 4 8 8 8 323
+7302 64 4 96 792 24 8 6
+7303 6 23 15 88 9 8 7
+7304 10 11 4 463 8 13 73
+7305 10 11 4 8 8 556 2
+7306 6 1005 5 16 11 8 7
+7307 83 608 155 793 1 1 17
+7308 10 1006 4 8 8 8 2
+7309 6 5 4 8 628 8 2
+7310 6 4 12 1 20 12 526
+7311 6 4 12 16 629 7 7
+7312 6 4 3 794 11 8 6
+7313 64 7 1 1 614 8 6
+7314 6 11 4 249 8 8 2
+7315 136 11 4 1 9 18 7
+7316 48 46 43 45 11 557 35
+7317 10 11 5 12 8 18 2
+7318 685 11 4 8 8 8 2
+7319 10 11 4 8 630 8 2
+7320 129 354 624 13 30 14 13
+7321 10 11 4 8 8 8 527
+7322 6 1007 14 16 24 8 14
+7323 10 11 4 795 8 8 405
+7324 6 95 3 18 9 558 6
+7325 54 22 4 342 40 16 4
+7326 6 133 12 1 9 5 7
+7327 686 11 4 8 8 8 133
+7328 35 132 2 796 37 5 4
+7329 6 4 14 16 358 8 14
+7330 687 103 19 36 23 44 26
+7331 10 11 4 8 631 8 2
+7332 6 1008 362 52 632 50 528
+7333 688 4 12 1 20 13 7
+7334 689 11 4 8 8 13 73
+7335 6 4 4 797 43 8 6
+7336 6 4 7 45 11 239 7
+7337 10 11 4 8 633 8 2
+7338 136 1009 5 1 8 18 2
+7339 27 32 24 29 26 9 22
+7340 13 40 19 13 23 559 109
+7341 238 52 10 13 17 25 17
+7342 20 45 41 798 5 32 2
+7343 8 7 625 8 8 8 6
+7344 76 43 19 14 18 68 529
+7345 51 48 328 374 34 42 37
+7346 690 43 9 37 17 37 25
+7347 484 48 467 266 34 42 37
+7348 51 649 220 47 235 42 37
+7349 691 48 220 799 235 42 37
+7350 51 48 220 266 235 42 37
+7351 488 1010 470 800 448 414 530
+7352 10 11 4 12 8 45 67
+7353 6 11 4 10 7 560 6
+7354 6 1011 4 801 634 8 6
+7355 6 1011 4 802 634 8 6
+7356 6 1011 4 802 635 8 6
+7357 6 1011 4 802 634 241 6
+7358 692 37 29 25 4 5 73
+7359 6 402 14 16 358 2 14
+7360 6 11 626 803 7 8 6
+7361 6 4 12 18 24 8 6
+7362 693 1012 193 804 636 561 142
+7363 68 80 627 45 7 54 7
+7364 694 4 1 5 1 1 5
+7365 695 111 85 483 109 149 75
+7366 112 11 5 12 8 7 86
+7367 6 685 4 8 8 8 2
+7368 10 11 4 8 8 8 81
+7369 10 11 4 805 8 8 2
+7370 6 11 4 8 637 8 2
+7371 1 988 1 5 1 1 51
+7372 11 63 628 1 14 7 7
+7373 11 63 7 552 14 7 7
+7374 67 77 629 69 5 1 59
+7375 1 4 1 735 1 1 1
+7376 10 11 4 8 8 8 531
+7377 207 389 260 254 301 554 2
+7378 1 4 1 806 1 1 5
+7379 1 4 1 5 1 562 51
+7380 1 1013 1 5 6 1 5
+7381 1 4 1 807 1 1 5
+7382 501 23 630 808 329 309 2
+7383 696 4 1 5 1 1 5
+7384 6 61 6 11 13 563 50
+7385 1 10 1 1 1 1 532
+7386 6 11 4 8 80 8 2
+7387 6 27 159 10 112 1 2
+7388 13 14 19 36 638 11 10
+7389 13 14 631 36 23 11 10
+7390 697 14 19 36 23 11 10
+7391 13 40 93 13 23 28 122
+7392 53 40 632 13 36 28 29
+7393 53 1015 47 13 36 28 29
+7394 6 23 3 18 9 7 7
+7395 35 37 29 25 4 564 73
+7396 53 40 633 13 36 28 29
+7397 358 1016 15 16 9 8 7
+7398 16 4 634 16 9 7 7
+7399 53 40 635 13 36 28 29
+7400 6 4 33 16 11 7 14
+7401 21 35 27 6 5 565 4
+7402 10 374 5 10 8 8 2
+7403 698 1017 380 320 268 17 286
+7404 603 4 33 16 11 8 6
+7405 457 6 33 131 24 8 7
+7406 603 4 12 1 20 18 7
+7407 8 7 1 8 125 211 6
+7408 603 4 12 1 20 12 7
+7409 383 23 109 8 8 8 2
+7410 429 19 33 26 11 8 6
+7411 10 11 478 8 8 250 2
+7412 429 556 32 317 43 1 2
+7413 19 23 636 24 21 2 16
+7414 163 1018 85 189 280 275 75
+7415 163 393 637 809 68 246 75
+7416 51 48 220 47 34 277 37
+7417 16 4 12 16 639 7 7
+7418 6 4 127 810 24 8 6
+7419 11 1019 7 1 14 7 7
+7420 6 4 33 132 20 8 7
+7421 76 24 13 811 23 76 79
+7422 36 1020 9 13 17 11 25
+7423 12 1021 8 12 15 2 2
+7424 10 553 4 1 8 8 2
+7425 290 54 4 324 35 40 223
+7426 21 35 27 748 5 5 4
+7427 6 2 519 627 180 16 433
+7428 9 19 15 18 9 8 6
+7429 92 4 638 96 70 58 2
+7430 92 4 87 812 70 58 2
+7431 12 12 639 12 15 2 2
+7432 699 4 3 17 7 7 6

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/fumC.tfa

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/fumC.tfa

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/fumC.tfa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/fumC.tfa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,9625 @@
+>fumC_1
+CGAGCGCCATTCGTCAGGCTGCGGATGAAGTGCTGGCGGGGCAGCATGATGATGAATTCC
+CGCTGGCAATCTGGCAGACCGGTTCTGGCACACAAAGTAACATGAACATGAACGAAGTGC
+TGGCCAATCGGGCGAGTGAACTGCTCGGCGGCGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGATGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CGCTGAGTGAAAAATCGCGTGCATTTGCCGATATCGTAAAAATCGGTCGAACCCACTTGC
+AGGACGCCACGCCGCTAACACTGGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_2
+CGAGCGCCATTCGTCAGGCGGCGGATGAAGTACTGGCAGGACAGCATAACGATGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAATATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTTGGCGGCGTGCGCGGGATGGAGCGTAAAGTTCATC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAATGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAATCCCTGACACAGA
+CGCTGAGTGAAAAATCGCGCGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGC
+AGGATGCCACGCCGCTAACACTAGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTGGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCGCATGTAGCGGAACTGGC
+>fumC_3
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CATTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAATATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTTGGCGGCGTGCGCGGGATGGAGCGTAAAGTTCATC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAATGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCACAACTTAAAACCCTGACCCAGA
+CGCTGAGTGAAAAATCGCGCGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGC
+AGGATGCCACGCCGCTAACACTGGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTGGAGC
+ATAATCTCAAACATATTGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_4
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGCGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CACTGAGTGAAAAATCGCGTGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGC
+AGGACGCCACGCCGCTAACACTAGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_5
+CGAGCGCCATTCGTCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGTGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCTCAGCTTAAAACCCTGACACAGA
+CACTGAATGAGAAATCCCGTGCTTTTGCCGATATCGTCAAAATTGGTCGTACTCACTTGC
+AGGATGCCACGCCGTTAACGCTGGGGCAGGCGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_6
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGCGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CGCTGAGTGAAAAATCGCGTGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGC
+AGGACGCCACGCCGCTAACACTAGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_7
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGCGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CGCTGAGTGAAAAATCGCGTGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGC
+AGGACGCCACGCCGCTAACACTGGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGT
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_8
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGTGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGCTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CACTGAATGAGAAATCCCGTGCA..TGCCTCACGTAGCGGAACTGGC
+>fumC_1173
+CGAGCGCCATTCGTCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAATATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGCGTGCGTGGGATGGAGCGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCTAACGATGTCTTTCCAACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CACTGAATGAGAAATCGCGCGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGC
+AGGATGCCACGCCGCTAACACTGGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_1174
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGCGTGCGCGGGATGGAGCGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CGCTGAGTGAAAAATCGCGTGCATTTGCCGATATCGTAAAAATCGGTCGAACCCACTTGC
+AGGACGCCACGCCGCTAACACTGGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_1175
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCAGCGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CACTGAGTGAAAAATCGCGTGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGC
+AGGACGCCACGCCGCTAACACTAGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_1176
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCAGCTCCGGCACGCAAAGTAACATGAATATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGTGGCGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCACTACTGGCGCTGCGCAAGCAACTCATTCCACAACTTAAAACCCTGACCCAGA
+CGCTGAGTGAAAAATCCCGCGCATTTGCTGATATCGTCAAAATCGGTCGTACCCACTTGC
+AGGACGCCACGCCGTTAACGCTGGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTGGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_1177
+CGAGCGCCATTCGTCAGGCGGCGGATGAAGTACTGGCAGGGCAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGTGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGACGCTGCTGGCGCTGCGCAAGCAACTCATTCCTCAGCTTAAAACCCTGACACAGA
+CACTGAATGAGAAATCCCGTGCTTTTGCCGATATCGTCAAAATTGGTCGTACTCACTTGC
+AGGATGCCACGCCGTTAACGCTGGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_1178
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGGTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGTGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGCTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CACTGAATGAGAAATCCCGTGCATTTGCCGATATCGTCAAAATTGGTCGTACTCACTTGC
+AGGACGCCACGCCGCTAACACTAGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_1179
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGCGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCGCAGCTTAAAACCCTGACACAGA
+CACTGAGTGAAAAATCGCGTGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGC
+AGGACGCCACGCCGCTAACACTAGGGCAGGAGATTTTCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC
+>fumC_1180
+CGAGCGCCATTCGGCAGGCGGCGGATGAAGTACTGGCAGGACAGCATGACGACGAATTCC
+CGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGCGTGCGCGGGATGGAACGTAAAGTTCACC
+CTAACGACGACGTGAACAAAAGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACG
+TTGCGGCGCTGCTGGCGCTGCGCAAGCAACGCATTCCGCAGGTTAAAACCCTGACACAGA
+CACTGAGTGAAAAATCGCGTGCATTTGCCGATATCGTCAAAATCGGTCGAACCCACTTGC
+AGGACGCCACGCCGCTAACACTGGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGC
+ATAATCTCAAACATATCGAATACAGCCTGCCTCACGTAGCGGAACTGGC

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/gyrB.tfa

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/gyrB.tfa

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/gyrB.tfa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/gyrB.tfa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,5940 @@
+>gyrB_1
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCTCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGTGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCATCCGAATATCTTCTACTTCTCCACCGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_2
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCTAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGTGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAAGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCGAATATCTTCTACTTCTCCACCGAAAAAGATGGTATCGGCGTTGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_3
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAA
+GACCACTTCCACTATGAAGGTGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCGAATATCTTCTACTTCTCCACCGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_4
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCGAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_5
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCTCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCGAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_6
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATTCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCTCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGTGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAAGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCAAATATCTTCTACTTCTCCACCGAAAAAGACGGTATTGGCGTTGAA
+GTGGCGCTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_7
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCACCG
+TTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCGAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_8
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATTCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCACCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGTGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAAGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCAAATATCTTC..ACGCCGATCCACCCGAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_718
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGTGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGTCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCGAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_719
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCAAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_720
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGCTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCAAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_721
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGAAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCAAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCGAATATCTTCTACTTCTCCACCGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_722
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCTCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATAGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGTGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCATCCGAATATCTTCTACTTCTCCACCGAAAAAGACGGTATTGGCGTCGAA
+GTAGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_723
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCAAGCCTT
+GAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGATGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCAGAATATCTTCTACTTCTCCACCGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_724
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCTCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTC
+GAAACCTTCACCAATGTGACCGAGTTTGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTTAACTCCGGCGTTTCCATTCGCCTGCGCGACAAGCGTGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGTATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCAAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGTGTTGAA
+GTGGCGCTGCAGTGGAACGATGGCTTCCAGGAAAACATCT
+>gyrB_725
+GGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCTTGTCGCAAAAACTGGAGCTGGTT
+ATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCTAGCCTC
+GAAACTTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAG
+TTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAA
+GACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCGAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAA
+GTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCT

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/icd.tfa

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/icd.tfa

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/icd.tfa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/icd.tfa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,8980 @@
+>icd_1
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGATGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCTGTTGGTGG
+CGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAAAATTCG
+CTTCCCGGAACATTGTGGTATCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATC
+>icd_2
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGATGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCTGTTGGTGG
+CGGTATTCGTTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAGGGCGCCCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCAGGTATCGAATGGAAAGCTGATTC
+TGCCGACGCTGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAAAATTCG
+CTTCCCAGAACATTGTGGTATCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATC
+>icd_3
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTGG
+CGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATATATGCGGGTATCGAATGGAAAGCTGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGCGTGAAGAAAATTCG
+CTTCCCGGAACATTGCGGTATCGGTATTAAGCCGTGTTCTGAAGAAGGCACCAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATC
+>icd_4
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGATGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGCCCGCTGACCACTCCAGTAGGTGG
+CGGTATTCGTTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+CCCGGTACGTTACTATCAGGGCACCCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTAATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCTGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGCGTGAAGAAAATTCG
+CTTCCCGGAACATTGCGGTATCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCT
+GGTGCGTGCAGCGATCGAATACGCAATTGCGAACGATC
+>icd_5
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGATGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTACCATTAAAGGTCCGCTGACCACTCCTGTTGGTGG
+CGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAAAATTCG
+CTTCCCGGAACATTGTGGTATCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATC
+>icd_6
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTACGGTCAGGATGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGCCCTCTGACCACTCCGGTTGGTGG
+CGGTATTCGTTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAGGGCACCCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCTGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGCGTGAAGAAAATTCG
+CTTCCCGGAACATTGCGGCATCGGTATTAAGCCGTGTTCTGAAGAAGGTACCAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATC
+>icd_7
+CGACGCTGCAGTTGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGATGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCTGTTGGTGG
+CGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAAGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGCGTGAAGAAAATTCG
+CTTCCCGGAACATTGCGGTATCGGTATCAAGCCGTGTTCTGAAGAAGGCACCAAACGTCT
+GGTCCGTGCCGCGATTGAATACGCAATTGCCAA..GAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAAAATTCG
+CTTCCCGGAACATTGTGGTGTCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATC
+>icd_960
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTGG
+CGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAGCTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAAAATTCG
+CTTCCCGGAACATTGTGGTATCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATC
+>icd_961
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGTTGTCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGCCCGCTGACCACTCCGGTTGGTGG
+CGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGACAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCTGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGCGTGAAGAAAATTCG
+CTTCCCGGAACATTGCGGTATCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATC
+>icd_962
+CGACGCTGCAGTCGAGAAAGCCTATCAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGATGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCTATTAAAGGTCCGCTGACCACTCCTGTTGGTGG
+CGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAAGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGCGTGAAGAAAATTCG
+CTTCCCGGAACATTGCGGTATCGGTATCAAGCCGTGTTCTGAAGAAGGCACCAAACGTCT
+GGTCCGTGCCGCGATTGAATACGCAATTGCCAACGACC
+>icd_963
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCTATTAAAGGCCCGCTGACCACTCCGGTTGGTGG
+CGGTATTCGTTCTCTCAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAGGGCACCCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCAGGTATCGAATGGAAAGCTGACTC
+TGCCGACGCTGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGCGTGAAGAAAATTCG
+CTTCCCGGAACATTGCGGTATCGGTATTAAGCCGTGTTCAGAAGAAGGCACTAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCCAACGATC
+>icd_964
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCTGTTGGTGG
+CGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAAGGCAGTCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAAAATTCG
+CTTCCCGGAACATTGTGGTATCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCT
+GGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATC
+>icd_965
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGATGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCTGTTGGTGG
+CGGTATTCGTTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAAGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGTGTGAAGAAAATTCG
+CTTCCCGGAACATTGCGGTATCGGTATCAAGCCGTGTTCTGAAGAAGGCACCAAACGTCT
+GGTCCGTGCCGCGATTGAATACGCAATTGCCAACGACC
+>icd_966
+CGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTA
+CACCGGTGAAAAATCCACACAGGTTTATGGTCAGGATGTCTGGCTGCCTGCTGAAACCCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCTGTTGGTGG
+CGGTATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCG
+TCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATAT
+GGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAAAATTCG
+CTTCCCGGAACATTGTGGTATCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCT
+GGTTCGTGCAACGATCGAATACGCAATTGCTAACGATC

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/mdh.tfa

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/mdh.tfa

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/mdh.tfa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/mdh.tfa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,5975 @@
+>mdh_1
+GGTGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_2
+GGTGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATT
+ACTAACCCGGTTAACACCACAGTTGCGATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCTGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCTTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGCATCCAGAACGCGGGTACTGAAGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_3
+GGCGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCTTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_4
+GGTGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCGATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGTGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGCTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_5
+GGTGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCGATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGCTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_6
+GGCGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_7
+GGTGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCGATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_8
+GGCGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGCATCCAGAACGCGGGTACTGAAGTGGTTGAAGCGAAG
+GCCGGTGGCGGGTCTGCAACCCTGTCT..GGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_726
+GGTGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACTGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCTTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_727
+GGCGTAGCGCGTAAACCGGGTATGGATCGTTCCGGCCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGCATCCAGAACGCGGGTACTGAAGTGGTTGAAGCGAAG
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_728
+GGCGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGCATCCAGAACGCGGGTACTGAAGTGGTTGTAGCGAAG
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_729
+GGTGTGGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTTCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCGATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCAGGTACTGAAGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_730
+GGTGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACTTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACTGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTTGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCAGGTACTGAAGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_731
+GGTGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCGATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGTGTTAGCTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG
+>mdh_732
+GGTGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACTGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGCGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCAGGTACTGAAGTGGTTGAAGCGAAA
+GCCGGTGGTGGGTCTGCAACCCTGTCTATGGG
+>mdh_733
+GGCGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGTTTAACGTTAACGCCGGCATC
+GTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACTACAGTTGCGATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTT
+TATGACAAAAACAAACTGTTCGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTT
+GTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAGTGCCGGTTATTGGTGGTCAC
+TCTGGTGTTACCATTCTGCCGCTGCTGTCACTGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGTATCCAGAACGCGGGTACTGAGGTGGTTGAAGCGAAA
+GCCGGTGGCGGGTCTGCAACCCTGTCTATGGG

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/purA.tfa

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/purA.tfa

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/purA.tfa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/purA.tfa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,5535 @@
+>purA_1
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_2
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTCGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_3
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTCGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCAACTCGTGT
+>purA_4
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGATGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTCGAAGGTGCTCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_5
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTCGAAGGTGCTCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACATCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_6
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGCCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTCGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCAACTCGTGT
+>purA_7
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTAGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTATGTTCTGGGTATCCTCAAAGCTTACTCAACTCGTGT
+>purA_8
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTAGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGT..AAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCCACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTTGTTGACGTTTCTGATCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCACGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_647
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTAGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTTGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTTGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CATATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_648
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTCGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGTCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_649
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTAGCACGTCGCGGTCTGTGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTTGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CATATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_650
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GACCTGCTTATGAAGATAAAGTAGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_651
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTTCTTATGAAGATAAAGTAGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_652
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTGGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGGTGGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT
+>purA_653
+ATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGGCACCACCGGTCGTGGTATCG
+GGCCTGCTTATGAAGATAAAGTAGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTA
+ACTACTACAAAGCTGAAGCGTTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTG
+CCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCTGCTCGACCAGGCGCGTCAGC
+GTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCC
+TGGGCCCGCGTTATGTTGATTACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGT

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/recA.tfa

diff -r 000000000000 -r 8be2feb96994 data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/recA.tfa

data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/recA.tfa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/escherichia_coli_pubmlst_k31_2018-10-09/escherichia_coli_pubmlst_scheme_2018-10-09/recA.tfa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,5450 @@
+>recA_1
+CGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGTGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCACCGTTTAAACAGGCTGAATTTCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_2
+CGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_3
+CGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCCCTGACGCCGAAAGCGGAAATCGAAGGTGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_4
+TGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACTGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+TGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTATGGCGA
+>recA_5
+CGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGGGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATAATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCACCGTTTAAACAGGCTGAATTTCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_6
+CGCACGTAAACTGGGCGTCGATATCGATAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_7
+CGCACGTAAACTGGGCGTCGATATCGATAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCACCGTTTAAACAGGCTGAATTTCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_8
+CGCACGTAAACTGGGCGTCGATATCGATAACC..TGATGTT
+TGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACACCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_603
+CGCACGTAAACTGGGCGTCGATATCGATAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACATTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_604
+CGCACGTAAACTGGGCGTCGATATCGATAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAAGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAATCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCACCGTTTAAACAGGCTGAATTTCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_605
+CGCACGTAAACTGGGCGTCGATATCGATAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTAGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_606
+CGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATTCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_607
+CGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCTCTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_608
+TGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGCTCCCAGCCGGACACCGGCGA
+GCAGGCACTGGAAATCTGTGACGCTCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCAGAAATCGAAGGTGAAATCGGCGACTCTCA
+CATGGGCCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACGACTACCGGTGGTAACGCGCTGAAATTCTACGCTTCTGTTCGTCT
+CGATATCCGTCGCATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA
+>recA_609
+TGCTCGTAAACTGGGCGTCGATATCGACAACCTGCTGTGTTCCCAGCCGGACACTGGCGA
+ACAGGCGCTGGAAATCTGTGACGCCCTGGCGCGCTCTGGCGCAGTAGACGTTATCGTTGT
+TGACTCCGTAGCGGCACTGACGCCGAAAGCGGAAATCGAAGGTGAAATCGGCGACTCTCA
+CATGGGTCTTGCGGCACGTATGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAA
+GCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGTATGAAAATTGGTGTGATGTT
+CGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCG
+CGTGAAAGTGGTGAAGAACAAAATCGCTGCGCCGTTTAAACAGGCTGAGTTCCAGATCCT
+CTACGGCGAAGGTATCAACTTCTACGGCGA

data/stx.fa

diff -r 000000000000 -r 8be2feb96994 data/stx.fa

data/stx.fa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/stx.fa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,301 @@
+>stx1:1:M24352:1
+ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGGTTGCGAAGGAATTTACCTTAGACTTCTCGACCGCAAAGACGTATGTAGATTCGCTGAATGTCATTCGCTCTGCAATAGGTACTCCATTACAGACTATTTCATCAGGAGGTACGTCTTTACTGATGATTGATAGTGGCACAGGGGATAATTTGTTTGCAGTTGATGTCAGAGGGATAGATCCAGAGGAAGGGCGGTTTAATAATCTACGGCTTATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAATAATGTTTTTTATCGCTTTGCTGATTTTTCACATGTTACCTTTCCAGGTACAACAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAGCGTGTTGCAGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGTTGACTACTTCTTATCTGGATTTAATGTCGCATAGTGGAACCTCACTGACGCAGTCTGTGGCAAGAGCGATGTTACGGTTTGTTACTGTGACAGCTGAAGCTTTACGTTTTCGGCAAATACAGAGGGGATTTCGTACAACACTGGATGATCTCAGTGGGCGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAACTGGGGAAGGTTGAGTAGTGTCCTGCCTGACTATCATGGACAAGACTCTGTTCGTGTAGGAAGAATTTCTTTTGGAAGCATTAATGCAATTCTGGGAAGCGTGGCATTAATACTGAATTGTCATCATCATGCATCGCGAGTTGCCAGAATGGCATCTGATGAGTTTCCTTCTATGTGTCCGGCAGATGGAAGAGTCCGTGGGATTACGCACAATAAAATATTGTGGGATTCATCCACTCTGGGGGCAATTCTGATGCGCAGAACTATTAGCAGTTGAGGGGGTAAAATGAAAAAAACATTATTAATAGCTGCATCGCTTTCATTTTTTTCAGCAAGTGCGCTGGCGACGCCTGATTGTGTAACTGGAAAGGTGGAGTATACAAAATATAATGATGACGATACCTTTACAGTTAAAGTGGGTGATAAAGAATTATTTACCAACAGATGGAATCTTCAGTCTCTTCTTCTCAGTGCGCAAATTACGGGGATGACTGTAACCATTAAAACTAATGCCTGTCATAATGGAGGGGGATTCAGCGAAGTTATTTTTCGTTGA
+>stx1:2:AB030485:2
+ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGGTTGCGAAGGAATTTACCTTAGACTTCTCGACTGCAAAGACGTATGTAGATTCGCTGAATGTCATTCGCTCTGCAATAGGTACTCCATTACAGACTATTTCATCAGGAGGTACGTCTTTACTGATGATTGATAGTGGCACAGGGGATAATTTGTTTGCAGTTGATGTCAGAGGGATAGATCCAGAGGAAGGGCGGTTTAATAATCTACGGCTTATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAATAATGTTTTTTATCGCTTTGCTGATTTTTCACATGTTACCTTTCCAGGTACAACAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAGCGTGTTGCAGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGTTGACTACTTCTTATCTGGATTTAATGTCGCATAGTGGAACCTCACTGACGCAGTCTGTGGCAAGAGCGATGTTACGGTTTGTTACTGTGACAGCTGAAGCTTTACGTTTTCGGCAAATACAGAGGGGATTTCGTACAACACTGGATGATCTCAGTGGGCGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAACTGGGGAAGGTTGAGTAGTGTCCTGCCTGACTATCATGGACAAGACTCTGTTCGTGTAGGAAGAATTTCTTTTGGAAGCATTAATGCAATTCTGGGAAGCGTGGCATTAATACTGAATTGTCATCATCATGCATCGCGAGTTGCCAGAATGGCATCTGATGAGTTTCCTTCTATGTGTCCGGCAGATGGAAGAGTCCGTGGGATTACGCACAATAAAATATTGTGGGATTCATCCACTCTGGGGGCAATTCTGATGCGCAGAACTATTAGCAGTTGAGGGGGTAAAATGAAAAAAACATTATTAATAGCTGCATCGCTTTCATTTTTTTCAGCAAGTGCGCTGGCGACGCCTGATTGTGTAACTGGAAAGGTGGAGTATACAAAATATAATGATGACGATACCTTTACAGTTAAAGTGGGTGATAAAGAATTATTTACCAACAGATGGAATCTTCAGTCTCTTCTTCTCAGTGCGCAAATTACGGGGATGACTGTAACCATTAAAACTAATGCCTGTCATAATGGAGGGGGATTCAGCGAAGTTATTTTTCGTTGA
+>stx1:3:M19437:3
+ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGGTTGCGAAGGAATTTACCTTAGACTTCTCGACTGCAAAGACGTATGTAGATTCGCTGAATGTCATTCGCTCTGCAATAGGTACTCCATTACAGACTATTTCATCAGGAGGTACGTCTTTACTGATGATTGATAGTGGCACAGGGGATAATTTGTTTGCAGTTGATGTCAGAGGGATAGATCCAGAGGAAGGGCGGTTTAATAATCTACGGCTTATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAATAATGTTTTTTATCGCTTTGCTGATTTTTCACATGTTACCTTTCCAGGTACAACAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAGCGTGTTGCAGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGTTGACTACTTCTTATCTGGATTTAATGTCGCATAGTGGAACCTCACTGACGCAGTCTGTGGCAAGAGCGATGTTACGGTTTGTTACTGTGACAGCTGAAGCTTTACGTTTTCGGCAAATACAGAGGGGATTTCGTACAACACTGGATGATCTCAGTGGGCGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAACTGGGGAAGGTTGAGTAGTGTCCTGCCTGACTATCATGGACAAGACTCTGTTCGTGTAGGAAGAATTTCTTTTGGAAGCATTAATGCAATTCTGGGAAGCGTGGCATTAATACTGAATTGTCATCATCATGCATCGCGAGTTGCCAGAATGGCATCTGATGAGTTTCCTTCTATGTGTCCGGCAGATGGAAGAGTCCGTGGGATTACGCACAATAAAATATTGTGGGATTCATCCACTCTGGGGGCAATTCTGATGCGCAGAACTATTAGCAGTTGAGGGGGTAAAATGAAAAAAACATTATTAATAGCTGCATCGCTTTCATTTTTTTCAGCAAGTGCGCTGGCGACGCCTGATTGTGTAACTGGAAAGGTGGAGTATACAAAATATAATGATGACGATACCTTTACAGTTAAAGTGGGTGATAAAGAATTATTTACCAACAGATGGAATCTTCAGTCTCTTCTTCTCAGTGCGCAAATTACGGGGATGACTGTAACCATTAAAACTAATGCCTGTCATAATGGAGGGGGATTCAGCGAAGTTATTTTTCGTTGA
+>stx1:4:L04539:4
+ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGGTTGCGAAGGAATTTACCTTAGACTTCTCGACTGCAAAGACGTATGTAGATTCGCTGAATGTCAT..CTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGGATAATACCTTTACTGTGAAGGTGTCAGGAAGAGAATACTGGACGAACAGATGGAATTTGCAGCCATTGTTACAAAGTGCTCAGCTGACAGGGATGACTGTAACAATCATATCTAATACCTGCAGTTCAGGCTCAGGCTTTGCCCAGGTGAAGTTTAACTGA
+>stx2:STEC409
+ATGAAGTGTATATTATTTAAATGGGTGCTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCAGGAGTTTACGATAGACTTTTCGACTCAACAAAGTTATGTATCTTCGTTAAATAGTATACGGACAGCGATATCGACCCCTCTTGAACATATATCTCAGGGAGCTACATCGGTATCCGTTATTAATCATACACCACCAGGAAGTTATATTTCCGTAGGTATACGAGGGCTTGATGTTTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACAGATTTTCAGATTTTGCACATATATCATTGCCCGGTGTGACAACTATTTCCATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGAGGCTTCTAGGGCTGTCCTGCGTTTTGTAACCGTCACAGCCGAAGCCTTACGGTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACAGCTCCTGTTTATACGATGACGCCGGAAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAACATATCAGCGATACTTGGTACTGTGGCCGTTATACTGAATTGCTATCATCAGGGCGCGCGTTCTGTTCGCGCTGTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATACAGCAGCAGCGTTTCTGAACAGAAAGTCACAGTCTTTATATACAACGGGTGAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGAACGATACATTCACAGTAAAAGTGGCCGGGAAAGAGTACTGGACTAACCGCTGGAATCTGCAACCGCTACTGCAAAGTGCACAGTTAACAGGAATGACAGTCACAATCAAGTCCAGTACCTGTGCATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>stx2:STEC309
+ATGAAGTGTATATTATTTAAATGGGTGCTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCAGGAGTTTACGATAGACTTTTCGACTCAACAAAGTTATGTATCTTCGTTAAATAGTATACGGACAGCGATATCGACCCCTCTTGAACATATATCTCAGGGAGCTACATCGGTATCCGTTATTAATCATACACCACCAGGAAGTTATATTTCCGTAGGTATACGAGGGCTTGATGTTTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACAGATTTTCAGATTTTGCACATATATCATTGCCCGGTGTGACAACTATTTCCATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGAGGCTTCTAGGGCTGTCCTGCGTTTTGTAACCGTCACAGCCGAAGCCTTACGGTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACAGCTCCTGTTTATACGATGACGCCGGAAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAACATATCAGCGATACTTGGTACTGTGGCCGTTATACTGAATTGCCATCATCAGGGCGCGCGTTCTGTTCGCGCTGTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATACAGCAGCAGCGTTTCTGAACAGAAAGTCACAGTCTTTATATACAACGGGTGAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGAACGATACATTCACAGTAAAAGTGGCCGGGAAAGAGTACTGGACTAACCGCTGGAATCTGCAACCGCTACTGCAAAGTGCACAGTTAACAGGAATGACAGTCACAATCAAGTCCAGTACCTGTGCATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>stx2:STEC388
+ATGAAGTGTATATTATTTAAATGGGTACTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCAGGAGTTTACGATAGACTTTTCGACTCAACAAAGTTATGTATCTTCGTTAAATAGTATACGGACAGCGATATCGACCCCTCTTGAACATATATCTCAGGGAGCTACATCGGTATCCGTTATTAATCATACACCACCAGGAAGTTATATTTCCGTAGGTATACGAGGGCTTGATGTTTATCAGGCGCATTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACAGATTTTCAGATTTTGCACATATATCATTGCCCGGTGTGACAACTATTTCCATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGAGGCTTCTAGGGCTGTCCTGCGTTTTGTAACCGTCACAGCCGAAGCCTTACGGTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACAGCTCCTGTTTATACGATGACGCCGGAAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAACATATCAGCGATACTTGGTACTGTGGCCGTTATACTGAATTGCCATCATCAGGGCGCGCGTTCTGTTCGCGCTGTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATACAGCAGCAGCGTTTCTGAACAGAAAGTCACAGTCTTTATATACAACGGGTGAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGAACGATACATTCACAGTAAAAGTGGCCGGGAAAGAGTACTGGACTAACCGCTGGAATCTGCAACCGCTACTGCAAAGTGCACAGTTAACAGGAATGACAGTCACAATCAAGTCCAGTACCTGTGCATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA

data/stx.nhr

diff -r 000000000000 -r 8be2feb96994 data/stx.nhr

data/stx.nhr

Binary file data/stx.nhr has changed

data/stx.nin

diff -r 000000000000 -r 8be2feb96994 data/stx.nin

data/stx.nin

Binary file data/stx.nin has changed

data/stx.nsq

diff -r 000000000000 -r 8be2feb96994 data/stx.nsq

data/stx.nsq

Binary file data/stx.nsq has changed

data/stx1.fa

diff -r 000000000000 -r 8be2feb96994 data/stx1.fa

data/stx1.fa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/stx1.fa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,51 @@
+>stx1a:1:M24352:1
+ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGGTTGCGAAGGAATTTACCTTAGACTTCTCGACCGCAAAGACGTATGTAGATTCGCTGAATGTCATTCGCTCTGCAATAGGTACTCCATTACAGACTATTTCATCAGGAGGTACGTCTTTACTGATGATTGATAGTGGCACAGGGGATAATTTGTTTGCAGTTGATGTCAGAGGGATAGATCCAGAGGAAGGGCGGTTTAATAATCTACGGCTTATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAATAATGTTTTTTATCGCTTTGCTGATTTTTCACATGTTACCTTTCCAGGTACAACAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAGCGTGTTGCAGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGTTGACTACTTCTTATCTGGATTTAATGTCGCATAGTGGAACCTCACTGACGCAGTCTGTGGCAAGAGCGATGTTACGGTTTGTTACTGTGACAGCTGAAGCTTTACGTTTTCGGCAAATACAGAGGGGATTTCGTACAACACTGGATGATCTCAGTGGGCGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAACTGGGGAAGGTTGAGTAGTGTCCTGCCTGACTATCATGGACAAGACTCTGTTCGTGTAGGAAGAATTTCTTTTGGAAGCATTAATGCAATTCTGGGAAGCGTGGCATTAATACTGAATTGTCATCATCATGCATCGCGAGTTGCCAGAATGGCATCTGATGAGTTTCCTTCTATGTGTCCGGCAGATGGAAGAGTCCGTGGGATTACGCACAATAAAATATTGTGGGATTCATCCACTCTGGGGGCAATTCTGATGCGCAGAACTATTAGCAGTTGAGGGGGTAAAATGAAAAAAACATTATTAATAGCTGCATCGCTTTCATTTTTTTCAGCAAGTGCGCTGGCGACGCCTGATTGTGTAACTGGAAAGGTGGAGTATACAAAATATAATGATGACGATACCTTTACAGTTAAAGTGGGTGATAAAGAATTATTTACCAACAGATGGAATCTTCAGTCTCTTCTTCTCAGTGCGCAAATTACGGGGATGACTGTAACCATTAAAACTAATGCCTGTCATAATGGAGGGGGATTCAGCGAAGTTATTTTTCGTTGA
+>stx1a:3:M19437:3
+ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGGTTGCGAAGGAATTTACCTTAGACTTCTCGACTGCAAAGACGTATGTAGATTCGCTGAATGTCATTCGCTCTGCAATAGGTACTCCATTACAGACTATTTCATCAGGAGGTACGTCTTTACTGATGATTGATAGTGGCACAGGGGATAATTTGTTTGCAGTTGATGTCAGAGGGATAGATCCAGAGGAAGGGCGGTTTAATAATCTACGGCTTATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAATAATGTTTTTTATCGCTTTGCTGATTTTTCACATGTTACCTTTCCAGGTACAACAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAGCGTGTTGCAGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGTTGACTACTTCTTATCTGGATTTAATGTCGCATAGTGGAACCTCACTGACGCAGTCTGTGGCAAGAGCGATGTTACGGTTTGTTACTGTGACAGCTGAAGCTTTACGTTTTCGGCAAATACAGAGGGGATTTCGTACAACACTGGATGATCTCAGTGGGCGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAACTGGGGAAGGTTGAGTAGTGTCCTGCCTGACTATCATGGACAAGACTCTGTTCGTGTAGGAAGAATTTCTTTTGGAAGCATTAATGCAATTCTGGGAAGCGTGGCATTAATACTGAATTGTCATCATCATGCATCGCGAGTTGCCAGAATGGCATCTGATGAGTTTCCTTCTATGTGTCCGGCAGATGGAAGAGTCCGTGGGATTACGCACAATAAAATATTGTGGGATTCATCCACTCTGGGGGCAATTCTGATGCGCAGAACTATTAGCAGTTGAGGGGGTAAAATGAAAAAAACATTATTAATAGCTGCATCGCTTTCATTTTTTTCAGCAAGTGCGCTGGCGACGCCTGATTGTGTAACTGGAAAGGTGGAGTATACAAAATATAATGATGACGATACCTTTACAGTTAAAGTGGGTGATAAAGAATTATTTACCAACAGATGGAATCTTCAGTCTCTTCTTCTCAGTGCGCAAATTACGGGGATGACTGTAACCATTAAAACTAATGCCTGTCATAATGGAGGGGGATTCAGCGAAGTTATTTTTCGTTGA
+>stx1a:4:L04539:4
+ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGGTTGCGAAGGAATTTACCTTAGACTTCTCGACTGCAAAGACGTATGTAGATTCGCTGAATGTCATTCGCTCTGCAATAGGTACTCCATTACAGACTATTTCATCAGGAGGTACGTCTTTACTGATGATTGATAGTGGCACAGGGGATAATTTGTTTGCAGTTGATGTCAGAGGGATAGATCCAGAGGAAGGGCGGTTTAATAATCTACGGCTTATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAATAATGTTTTTTATCGCTTTGCTGATTTTTCACATGTTACCTTTCCAGGTACAACAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAGCGTGTTGCAGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGTTGACTACTTCTTATCTGGATTTAATGTCGCATAGTGGAACCTTACTGACGCAGTCTGTGGCAAGAGCGATGTTACGGTTTGTTACTGTGACAGCTGAAGCTTTACGTTTTCGGCAAATACAGAGGGGATTTCGTACAACACTGGATGATCTCAGTGGGCGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAACTGGGGAAGGTTGAGTAGTGTCCTGCCTGATTATCATGGACAAGACTCTGTTCGTGTAGGAAGAATTTCTTTTGGAAGCATTAATGCAATTCTGGGAAGCGTGGCATTAATACTGAATTGTCATCATCATGCATCGCGAGTTGCCAGAATGGCATCTGATGAGTTTCCTTCTATGTGTCCGGCAGATGGAAGAGTCCGTGGGATTACGCACAATAAAATATTGTGGGATTCATCCACTCTGGGGGCAATTCTGATGCGCAGAACTATTAGCAGTTGAGGGGGTAAAATGAAAAAAACATTATTAATAGCTGCATCGCTTTCATTTTTTTCAGCAAGTGCGCTGGCGACGCCTGATTGTGTAACTGGAAAGGTGGAGTATACAAAATATAATGATGACGATACCTTTACAGTTAAAGTGGGTGATAAAGAATTATTTACCAACAGATGGAATCTTCAGTCTCTTCTTCTCAGTGCGCAAATTACGGGGATGACTGTAACCATTAAAACTAATGCCTGTCATAATGGAGGGGGATTCAGCGAAGTTATTTTTCGTTGA
+>stx1a:5:Z36900:5
+ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGGTTGCGAAGGAATTTACCTTAGACTTCTCGACTGCAAAGACGTATGTAGATTCGCTGAATGTC..CACTTTCATTTCTTTCAGCAAGTGTTCTGGCAGCGCCAGATTGTGTAACCGGAAAGGTGGAGTATACAAAATATAATGATGACGATACTTTTACAGTTAAAGTGGCAGATAAAGAATTATTTACTAACAGATGGAATCTTCAGTCTCTTCTTCTAAGTGCACAAATTACGGGGATGACGGTAACTATTAAGACTACTGCTTGTCATAATGGAGGGGGATTCAGCGAGGTTATTTTTCGTTGA
+>stx1d:22:AB050959:22
+ATGAAAATAATGATTTTTAGGGCGCTAACATTTTTCTTCGTTATCTTTTCAGTTAATGCGATTGCTAAGGAGTTTACCTTAGATTTCTCAACAGCAAAGAAGTATGTTGATTCGCTGAATGTCATTCGCTCTGCAATAGGTACGCCATTACAGACTATTTCATCGGGAGGTACATCTTTACTGATGATTGATAGTGGCACAGGCGATAATTTATTTGCAGTCGATATCATGGGGTTAGAACCAGAGGAAGAGCGGTTTAACAATCTACGACTGATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAACAATGTTTTTTATCGCTTTGCTGATTTTTCACATGTTACCTTTCCTGGTACAAGAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAGCGTGTTGCGGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGCTGACTACCTCTTATCTGGATTTGATGTCGTATAGCGGAACCTCACTGACGCAGTCTGTAGCAAGAGCAATGTTACGGTTTGTTACTGTGACAGCTGAAGCTTTGCGTTTTCGCCAAATCCAGAGGGGATTTCGTACAACACTTGATGATCTCAGTGGACGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAATTGGGGAAGACTGAGTAGTATTCTGCCCGACTATCATGGACAAGACTCCGTTCGTGTTGGAAGAATTTCTTTTGGGAGTATTAATGCAATTCTGGGAAGCGTGGCATTAATATTAAATTGCCATCATCATGCATCACGAGTTGCCAGAATGACACCTGATGAGTTTCCTTCTATGTGCCCGACAGATGGAAGTGGGCGTGGGATTACTCACAATAAAATATTGTGGGACTCATCTACACTGGGGGCAATTTTGATTCGCAGAACTATCAGTAGTTGAGGGGGTAAAATGAAAAAAGTATTATTAATAGCTGTTTCACTTTCATTTCTTTCAGCAAGTGTTCTGGCAGCGCCAGATTGTGTAACCGGAAAGGTGGAGTATACAAAATATAATGATGACGATACTTTTACAGTTAAAGTGGCAGATAAAGAATTATTTACTAACAGATGGAATCTTCAGTCTCTTCTTCTAAGTGCACAAATTACGGGGATGACGGTAACTATTAAGACTACTGCTTGTCATAATGGAGGGGGATTCAGCGAGGTTATTTTTCGTTGA
+>stx1d:23:AY986980:23
+ATGAAAATAATGATTTTTAGGGCGCTAACATTTTTCTTCGTTATCTTTTCAGTTAATGCGATTGCTAAGGAGTTTACCTTAGATTTCTCAACAGCAAAGAAGTATGTTGATTCGCTGAATGTCATTCGCTCTGCAATAGGTACGCCATTACAGACTATTTCATCGGGAGGTACATCTTTACTGATGATTGATAGTGGCACAGGCGATAATTTATTTGCAGTCGATATCATGGGGTTAGAACCAGAGGAAGAGCGGTTTAACAATCTACGACTGATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAACAATGTTTTTTATCGCTTTGCTGATTTTTCACATGTTACCTTTCCTGGTACAAGAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAGCGTGTTGCGGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGCTGACTACTTCTTATCTGGATTTGATGTCGTATAGCGGAACCTCACTGACGCAGTCTGTAGCAAGAGCAATGTTACGGTTTGTTACTGTGACAGCTGAAGCTTTGCGTTTTCGCCAAATCCAGAGGGGATTTCGTACAACACTTGATGATCTCAGTGGACGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAATTGGGGAAGACTGAGTAGTATTCTGCCCGACTATCATGGACAAGACTCCGTTCGTGTTGGAAGAATTTCTTTTGGGAGTATTAATGCAATTCTGGGAAGCGTGGCATTAATATTAAATTGCCATCATCATGCATCACGAGTTGCCAGAATGACACCTGATGAGTTTCCTTCTATGTGCCCGACAGATGGAAGTGGGCGTGGGATTACTCACAATAAAATATTGTGGGACTCATCTACACTGGGGGCAATTTTGATTCGCAGAACTATCAGTAGTTGAGGGGGTAAAATGAAAAAAGTATTATTAATAGCTGTTTCACTTTCATTTCTTTCAGCAAGTGTTCTGGCAGCGCCAGATTGTGTAACCGGAAAGGTGGAGTATACAAAATATAATGATGACGATACTTTTACGGTTAAAGTGGCAGATAAAGAATTATTTACTAACAGATGGAATCTTCAGTCTCTTCTTCTAAGTGCACAAATTACGGGGATGACGGTAACTATTAAGACTACTGCTTGTCATAATGGAGGGGGATTCAGCGAGGTTATTTTTCGTTGA
+>stx1d:24:AY170851:24
+ATGAAAATAATGATTTTTAGGGCGCTAACATTTTTCTTCGTTATCTTTTCAGTTAATGCGATTGCTAAGGAGTTTACCTTAGATTTCTCAACAGCAAAGAAGTATGTTGATTCGCTGAATGTCATTCGCTCTGCAATAGGTACGCCATTACAGACTATTTCATCGGGAGGTACATCTTTACTGATGATTGATAGTGGCACAGGCGATAATTTATTTGCAGTCGATATCATGGGGTTAGAACCAGAGGAAGAGCGGTTTAACAATCTACGACTGATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAACAATGTTTTTTATCGCTTTGCTGATTTTTCACACGTTACCTTTCCTGGTACAAGAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAGCGTGTTGCGGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGCTGACTACTTCTTATCTGGATTTGATGTCGTATAGCGGAACCTCACTGACGCAGTCTGTAGCAAGAGCAATGTTACGGTTTGTTACTGTGACAGCTGAAGCTTTGCGTTTTCGCCAAATCCAGAGGGGATTTCGTACAACACTTGATGATCTCAGTGGACGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAATTGGGGAAGACTGAGTAGTATTCTGCCCGACTATCATGGACAAGACTCCGTTCGTGTTGGAAGAATTTCTTTTGGGAGTATTAATGCAATTCTGGGAAGCGTGGCATTAATATTAAATTGCCATCATCATGCATCACGAGTTGCCAGAATGACACCTGATGAGTTTCCTTCTATGTGCCCGACAGATGGAAGTGGGCGTGGGATTACTCACAATAAAATATTGTGGGACTCATCTACACTGGGGGCAATTTTGATTCGCAGAACTATCAGTAGTTGAGGGGGTAAAATGAAAAAAGTATTATTAATAGCTGTTTCACTTTCATTTCTTTCAGCAAGTGTTCTGGCAGCGCCAGATTGTGTAACCGGAAAGGTGGAGTATACAAAATATAATGATGACGATACTTTTACAGTTAAAGTGGCAGATAAAGAATTATTTACTAACAGATGGAATCTTCAGTCTCTTCTTCTAAGTGCACAAATTACGGGGATGACGGTAACTATTAAGACCACTGCTTGTCATAATGGAGGGGGATTCAGCGAGGTTATTTTTCGTTGA

data/stx2.fa

diff -r 000000000000 -r 8be2feb96994 data/stx2.fa

data/stx2.fa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/stx2.fa Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,249 @@
+>stx2a:1:FM998851:1
+ATGAAGTGTATATTATTTAAATGGGTACTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCGGGAATTTACGATAGACTTTTCGACTCAACAAAGTTATGTCTCTTCGTTAAATAGTATACGGACAGAGATATCGACCCCTCTTGAACATATATCTCAGGGGACCACATCGGTGTCTGTTATTAACCACACCCCGCCGGGCAGTTATTTTGCTGTGGATATACGAGGGCTTGATGTCTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACCGTTTTTCAGATTTTACACATATATCAGTGCCCGGTGTGACAACGGTTTCCATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGATGCATCCAGAGCAGTTCTGCGTTTTGTCACTGTCACAGCAGAAGCCTTACGCTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACTGCTCCTGTGTATACGATGACGCCGGGAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAATATATCAGCGATACTGGGTACTGTGGCCGTTATACTGAATTGCCATCATCAGGGGGCGCGTTCTGTTCGCGCCGTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATACAGCAGCAGCGTTTCTGAACAGAAAGTCACAGTTTTTATATACAACGGGTAAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGGATGACACATTTACAGTGAAGGTTGACGGGAAAGAATACTGGACCAGTCGCTGGAATCTGCAACCGTTACTGCAAAGTGCTCAGCTGACAGGAATGACTGTCACAATCAAATCCAGTACCTGTGAATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>stx2a:2:AY443054:2
+ATGAAGTGTATATTATTTAAATGGGTACTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCGGGAGTTTACGATAGACTTTTCGACCCAACAAAGTTATGTCTCTTCGTTAAATAGTATACGGACAGAGATATCGACCCCTCTTGAACATATATCTCAGGGGACCACATCGGTGTCTGTTATTAACCACACCCCACCGGGCAGTTATTTTGCTGTGGATATACGAGGGCTTGATGTCTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACCGTTTTTCAGATTTTACACATATATCAGTGCCCGGTGTGACAACGGTTTCCATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGATGCATCCAGAGCAGTTCTGCGTTTTGTCACTGTCACAGCAGAAGCCTTACGCTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACTGCTCCTGTGTATACGATGACGCCGGGAGATGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAATATATCAGCGATACTGAGTACTGTGGCCGTTATACTGAATTGCCATCATCAGGGGGCGCGTTCTGTTCGCGCCGTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATACAGCAGCAGCGTTTCTGAACAGAAAGTCACAGTTTTTATATACAACGGGTAAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTGGTTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGGATGACACATTTACAGTGAAGGTTGACGGGAAAGAATACTGGACCAGTCGCTGGAATCTGCAACCGTTACTGCAAAGTGCTCAGCTGACAGGAATGACTGTCACAATCAAATCCAGTACCTGTGAATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>stx2a:3:GQ429162:3
+ATGAAGTGTATATTATTTAAATGGGTACTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCGGGAATTTACGATAGACTTTTCGACTCAACAAAGTTATGTCTCTTCGTTAAATAGTATACGGACAGAGATATCGACCCCTCTTGAACATATATCTCAGGGGACCACATCGGTGTCTGTTATTAACCACACCCCGCCGGGCAGTTATTTTGCTGTGGATATACGAGGGCTTGATGTCTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACCGTTTTTCAGATTTTACACATATATCAGTGCCCGGTGTGACAACGGTTTCCATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGATGCATCCAGAGCAGTTCTGCGTTTTGTCACTGTCACAGCAGAAGCCTTACGCTTCAGGCAGATACAGAGAGAATTTCGTCAGGTACTGTCTGAAACTGCTCCTGTGTATACGATGACGCCGGGAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAATATATCAGCGATACTGAGTACTGTGGCCGTTATACTGAATTGCCATCATCAGGGGGCGCGTTCTGTTCGCGCCGTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATACAGCAGCAGCGTTTCTGAACAGAAAGTCACAGTTTTTATATACAACGGGTAAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTGGTTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGGATGACACATTTACAGTGAAGGTTGACGGGAAAGAATACTGGACCAGTCGCTGGAATCTGCAACCGTTACTGCAAAGTGCTCAGCTGACAGGAATGACTGTCACAATCAAATCCAGTACCTGTGAATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>stx2a:4:FM998852:4
+ATGAAGTGTATATTATTTAAATGGGTACTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCGGGAA..AATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGGATAATACCTTTACTGTGAAGGTGTCAGGAAGAGAATACTGGACGAACAGATGGAATTTGCAGCCATTGTTACAAAGTGCTCAGCTGACAGGGATGACTGTAACAATCATATCTAATACCTGCAGTTCAGGCTCAGGCTTTGCCCAGGTGAAGTTTAACTGA
+>stx2k:STEC409
+ATGAAGTGTATATTATTTAAATGGGTGCTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCAGGAGTTTACGATAGACTTTTCGACTCAACAAAGTTATGTATCTTCGTTAAATAGTATACGGACAGCGATATCGACCCCTCTTGAACATATATCTCAGGGAGCTACATCGGTATCCGTTATTAATCATACACCACCAGGAAGTTATATTTCCGTAGGTATACGAGGGCTTGATGTTTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACAGATTTTCAGATTTTGCACATATATCATTGCCCGGTGTGACAACTATTTCCATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGAGGCTTCTAGGGCTGTCCTGCGTTTTGTAACCGTCACAGCCGAAGCCTTACGGTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACAGCTCCTGTTTATACGATGACGCCGGAAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAACATATCAGCGATACTTGGTACTGTGGCCGTTATACTGAATTGCTATCATCAGGGCGCGCGTTCTGTTCGCGCTGTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATACAGCAGCAGCGTTTCTGAACAGAAAGTCACAGTCTTTATATACAACGGGTGAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGAACGATACATTCACAGTAAAAGTGGCCGGGAAAGAGTACTGGACTAACCGCTGGAATCTGCAACCGCTACTGCAAAGTGCACAGTTAACAGGAATGACAGTCACAATCAAGTCCAGTACCTGTGCATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>stx2k:STEC309
+ATGAAGTGTATATTATTTAAATGGGTGCTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCAGGAGTTTACGATAGACTTTTCGACTCAACAAAGTTATGTATCTTCGTTAAATAGTATACGGACAGCGATATCGACCCCTCTTGAACATATATCTCAGGGAGCTACATCGGTATCCGTTATTAATCATACACCACCAGGAAGTTATATTTCCGTAGGTATACGAGGGCTTGATGTTTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACAGATTTTCAGATTTTGCACATATATCATTGCCCGGTGTGACAACTATTTCCATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGAGGCTTCTAGGGCTGTCCTGCGTTTTGTAACCGTCACAGCCGAAGCCTTACGGTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACAGCTCCTGTTTATACGATGACGCCGGAAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAACATATCAGCGATACTTGGTACTGTGGCCGTTATACTGAATTGCCATCATCAGGGCGCGCGTTCTGTTCGCGCTGTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATACAGCAGCAGCGTTTCTGAACAGAAAGTCACAGTCTTTATATACAACGGGTGAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGAACGATACATTCACAGTAAAAGTGGCCGGGAAAGAGTACTGGACTAACCGCTGGAATCTGCAACCGCTACTGCAAAGTGCACAGTTAACAGGAATGACAGTCACAATCAAGTCCAGTACCTGTGCATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>stx2k:STEC388
+ATGAAGTGTATATTATTTAAATGGGTACTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTCCCAGGAGTTTACGATAGACTTTTCGACTCAACAAAGTTATGTATCTTCGTTAAATAGTATACGGACAGCGATATCGACCCCTCTTGAACATATATCTCAGGGAGCTACATCGGTATCCGTTATTAATCATACACCACCAGGAAGTTATATTTCCGTAGGTATACGAGGGCTTGATGTTTATCAGGCGCATTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACAGATTTTCAGATTTTGCACATATATCATTGCCCGGTGTGACAACTATTTCCATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGAGGCTTCTAGGGCTGTCCTGCGTTTTGTAACCGTCACAGCCGAAGCCTTACGGTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACAGCTCCTGTTTATACGATGACGCCGGAAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAACATATCAGCGATACTTGGTACTGTGGCCGTTATACTGAATTGCCATCATCAGGGCGCGCGTTCTGTTCGCGCTGTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATACAGCAGCAGCGTTTCTGAACAGAAAGTCACAGTCTTTATATACAACGGGTGAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGAACGATACATTCACAGTAAAAGTGGCCGGGAAAGAGTACTGGACTAACCGCTGGAATCTGCAACCGCTACTGCAAAGTGCACAGTTAACAGGAATGACAGTCACAATCAAGTCCAGTACCTGTGCATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+

data/stxDB

diff -r 000000000000 -r 8be2feb96994 data/stxDB

data/stxDB

Binary file data/stxDB has changed

data/stxDB

diff -r 000000000000 -r 8be2feb96994 data/stxDB.dbtype

data/stxDB

Binary file data/stxDB.dbtype has changed

data/stxDB

diff -r 000000000000 -r 8be2feb96994 data/stxDB.index

data/stxDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/stxDB.index Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,145 @@
+0 0 1229
+1 1229 1243
+2 2472 1243
+3 3715 1243
+4 4958 1238
+5 6196 1229
+6 7425 1243
+7 8668 1243
+8 9911 1243
+9 11154 1238
+10 12392 1229
+11 13621 1243
+12 14864 1243
+13 16107 1243
+14 17350 1238
+15 18588 1229
+16 19817 1243
+17 21060 1243
+18 22303 1243
+19 23546 1238
+20 24784 1229
+21 26013 1243
+22 27256 1243
+23 28499 1243
+24 29742 1238
+25 30980 1229
+26 32209 1243
+27 33452 1243
+28 34695 1243
+29 35938 1238
+30 37176 1229
+31 38405 1243
+32 39648 1243
+33 40891 1243
+34 42134 1238
+35 43372 1229
+36 44601 1243
+37 45844 1243
+38 47087 1243
+39 48330 1238
+40 49568 1229
+41 50797 1243
+42 52040 1243
+43 53283 1243
+44 54526 1238
+45 55764 1229
+46 56993 1243
+47 58236 1243
+48 59479 1244
+49 60723 1238
+50 61961 1229
+51 63190 1243
+52 64433 1243
+53 65676 1244
+54 66920 1238
+55 68158 1229
+56 69387 1243
+57 70630 1243
+58 71873 1244
+59 73117 1238
+60 74355 1229
+61 75584 1243
+62 76827 1243
+63 78070 1244
+64 79314 1245
+65 80559 1229
+66 81788 1243
+67 83031 1243
+68 84274 1244
+69 85518 1237
+70 86755 1229
+71 87984 1243
+72 89227 1243
+73 90470 1244
+74 91714 1245
+75 92959 1230
+76 94189 1243
+77 95432 1243
+78 96675 1244
+79 97919 1245
+80 99164 1230
+81 100394 1243
+82 101637 1243
+83 102880 1244
+84 104124 1238
+85 105362 1230
+86 106592 1243
+87 107835 1243
+88 109078 1244
+89 110322 1230
+90 111552 1243
+91 112795 1243
+92 114038 1238
+93 115276 1230
+94 116506 1243
+95 117749 1243
+96 118992 1238
+97 120230 1229
+98 121459 1243
+99 122702 1243
+100 123945 1238
+101 125183 1229
+102 126412 1243
+103 127655 1243
+104 128898 1244
+105 130142 1229
+106 131371 1243
+107 132614 1243
+108 133857 1245
+109 135102 1229
+110 136331 1243
+111 137574 1243
+112 138817 1238
+113 140055 1243
+114 141298 1243
+115 142541 1243
+116 143784 1238
+117 145022 1243
+118 146265 1243
+119 147508 1243
+120 148751 1243
+121 149994 1243
+122 151237 1243
+123 152480 1243
+124 153723 1244
+125 154967 1243
+126 156210 1243
+127 157453 1243
+128 158696 1244
+129 159940 1243
+130 161183 1243
+131 162426 1243
+132 163669 1244
+133 164913 1243
+134 166156 1243
+135 167399 1246
+136 168645 1244
+137 169889 1243
+138 171132 1243
+139 172375 1243
+140 173618 1245
+141 174863 1243
+142 176106 1243
+143 177349 1243
+144 178592 1245

data/stxDB

diff -r 000000000000 -r 8be2feb96994 data/stxDB.lookup

data/stxDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/stxDB.lookup Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,145 @@
+0 stx1:1:M24352:1 0
+1 stx2:9:FM998839:9 0
+2 stx2:41:AM982821:41 0
+3 stx2:73:EF441605:73 0
+4 stx2:105:M29153:105 0
+5 stx1:2:AB030485:2 0
+6 stx2:10:Z37725:10 0
+7 stx2:42:AY633464:42 0
+8 stx2:74:EF584538:74 0
+9 stx2:106:X81418:106 0
+10 stx1:3:M19437:3 0
+11 stx2:11:FM998842:11 0
+12 stx2:43:AY633473:43 0
+13 stx2:75:AF329817:75 0
+14 stx2:107:AJ313016:107 0
+15 stx1:4:L04539:4 0
+16 stx2:12:Z50754:12 0
+17 stx2:44:AY633453:44 0
+18 stx2:76:AF500192:76 0
+19 stx2:108:FM998844:108 0
+20 stx1:5:Z36900:5 0
+21 stx2:13:AY443052:13 0
+22 stx2:45:AY633467:45 0
+23 stx2:77:AY095209:77 0
+24 stx2:109:U72191:109 0
+25 stx1:6:AB083044:6 0
+26 stx2:14:AJ272135:14 0
+27 stx2:46:AY633469:46 0
+28 stx2:78:DQ059012:78 0
+29 stx2:110:M21534:110 0
+30 stx1:7:AB035142:7 0
+31 stx2:15:AF524944:15 0
+32 stx2:47:AY739671:47 0
+33 stx2:79:SNS:79 0
+34 stx2:111:X81417:111 0
+35 stx1:8:AM230663:8 0
+36 stx2:16:FM998856:16 0
+37 stx2:48:DQ235774:48 0
+38 stx2:80:FN182287:80 0
+39 stx2:112:X81415:112 0
+40 stx1:9:AM230662:9 0
+41 stx2:17:FM998858:17 0
+42 stx2:49:AB071845:49 0
+43 stx2:81:FM998855:81 0
+44 stx2:113:X81416:113 0
+45 stx1:10:AJ279086:10 0
+46 stx2:18:EF441619:18 0
+47 stx2:50:AF461167:50 0
+48 stx2:82:AB012102:82 0
+49 stx2:114:FN182286:114 0
+50 stx1:11:Z36899:11 0
+51 stx2:19:AY633459:19 0
+52 stx2:51:AF291819:51 0
+53 stx2:83:AB048228:83 0
+54 stx2:115:FM998846:115 0
+55 stx1:12:AF461168:12 0
+56 stx2:20:GQ429170:20 0
+57 stx2:52:AB015057:52 0
+58 stx2:84:AB048238:84 0
+59 stx2:116:AY368993:116 0
+60 stx1:13:M19473:13 0
+61 stx2:21:AF461171:21 0
+62 stx2:53:AY443045:53 0
+63 stx2:85:AB048224:85 0
+64 stx2:117:AM939642:117 0
+65 stx1:14:AB048232:14 0
+66 stx2:22:AY443057:22 0
+67 stx2:54:AY633470:54 0
+68 stx2:86:AB048223:86 0
+69 stx2:118:FM998838:118 0
+70 stx1:15:AB071620:15 0
+71 stx2:23:AF461173:23 0
+72 stx2:55:AY443049:55 0
+73 stx2:87:AB048229:87 0
+74 stx2:119:AY332411:119 0
+75 stx1:16:AB048237:16 0
+76 stx2:24:AB030484:24 0
+77 stx2:56:FM998860:56 0
+78 stx2:88:AB012101:88 0
+79 stx2:120:AJ567998:120 0
+80 stx1:17:AB071622:17 0
+81 stx2:25:AY633472:25 0
+82 stx2:57:AY443047:57 0
+83 stx2:89:AB048226:89 0
+84 stx2:121:AJ249351:121 0
+85 stx1:18:AB071624:18 0
+86 stx2:26:EF441613:26 0
+87 stx2:58:AF479828:58 0
+88 stx2:90:AB048225:90 0
+89 stx1:19:DQ449666:19 0
+90 stx2:27:AY633471:27 0
+91 stx2:59:GQ429172:59 0
+92 stx2:91:AJ313015:91 0
+93 stx1:20:Z36901:20 0
+94 stx2:28:DQ344636:28 0
+95 stx2:60:AY633457:60 0
+96 stx2:92:AF043627:92 0
+97 stx1:21:AB050958:21 0
+98 stx2:29:EF441609:29 0
+99 stx2:61:AY633458:61 0
+100 stx2:93:AJ567997:93 0
+101 stx1:22:AB050959:22 0
+102 stx2:30:EF441599:30 0
+103 stx2:62:AY443048:62 0
+104 stx2:94:EF441616:94 0
+105 stx1:23:AY986980:23 0
+106 stx2:31:X07865:31 0
+107 stx2:63:FM998848:63 0
+108 stx2:95:AJ567995:95 0
+109 stx1:24:AY170851:24 0
+110 stx2:32:EF441618:32 0
+111 stx2:64:AF500191:64 0
+112 stx2:96:L11078:96 0
+113 stx2:1:FM998851:1 0
+114 stx2:33:EF441604:33 0
+115 stx2:65:EF441621:65 0
+116 stx2:97:X65949:97 0
+117 stx2:2:AY443054:2 0
+118 stx2:34:AY443044:34 0
+119 stx2:66:FM99884:66 0
+120 stx2:98:AM904726:98 0
+121 stx2:3:GQ429162:3 0
+122 stx2:35:L11079:35 0
+123 stx2:67:AF500190:67 0
+124 stx2:99:AB048227:99 0
+125 stx2:4:FM998852:4 0
+126 stx2:36:M59432:36 0
+127 stx2:68:DQ235775:68 0
+128 stx2:100:AY286000:100 0
+129 stx2:5:GQ429163:5 0
+130 stx2:37:FM177471:37 0
+131 stx2:69:AF479829:69 0
+132 stx2:101:AB048236:101 0
+133 stx2:6:GQ429168:6 0
+134 stx2:38:AF500189:38 0
+135 stx2:70:AY739671:70 0
+136 stx2:102:AJ966783:102 0
+137 stx2:7:FM998854:7 0
+138 stx2:39:AY443043:39 0
+139 stx2:71:EU816447:71 0
+140 stx2:103:AB472687:103 0
+141 stx2:8:FM998861:8 0
+142 stx2:40:EU086525:40 0
+143 stx2:72:X61283:72 0
+144 stx2:104:AJ010730:104 0

data/stxDB

diff -r 000000000000 -r 8be2feb96994 data/stxDB_h

data/stxDB

Binary file data/stxDB_h has changed

data/stxDB

diff -r 000000000000 -r 8be2feb96994 data/stxDB_h.dbtype

data/stxDB

Binary file data/stxDB_h.dbtype has changed

data/stxDB

diff -r 000000000000 -r 8be2feb96994 data/stxDB_h.index

data/stxDB

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/stxDB_h.index Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,145 @@
+0 0 18
+1 18 20
+2 38 22
+3 60 22
+4 82 22
+5 104 20
+6 124 20
+7 144 22
+8 166 22
+9 188 22
+10 210 18
+11 228 22
+12 250 22
+13 272 22
+14 294 24
+15 318 18
+16 336 20
+17 356 22
+18 378 22
+19 400 24
+20 424 18
+21 442 22
+22 464 22
+23 486 22
+24 508 22
+25 530 20
+26 550 22
+27 572 22
+28 594 22
+29 616 22
+30 638 20
+31 658 22
+32 680 22
+33 702 17
+34 719 22
+35 741 20
+36 761 22
+37 783 22
+38 805 22
+39 827 22
+40 849 20
+41 869 22
+42 891 22
+43 913 22
+44 935 22
+45 957 22
+46 979 22
+47 1001 22
+48 1023 22
+49 1045 24
+50 1069 20
+51 1089 22
+52 1111 22
+53 1133 22
+54 1155 24
+55 1179 22
+56 1201 22
+57 1223 22
+58 1245 22
+59 1267 24
+60 1291 20
+61 1311 22
+62 1333 22
+63 1355 22
+64 1377 24
+65 1401 22
+66 1423 22
+67 1445 22
+68 1467 22
+69 1489 24
+70 1513 22
+71 1535 22
+72 1557 22
+73 1579 22
+74 1601 24
+75 1625 22
+76 1647 22
+77 1669 22
+78 1691 22
+79 1713 24
+80 1737 22
+81 1759 22
+82 1781 22
+83 1803 22
+84 1825 24
+85 1849 22
+86 1871 22
+87 1893 22
+88 1915 22
+89 1937 22
+90 1959 22
+91 1981 22
+92 2003 22
+93 2025 20
+94 2045 22
+95 2067 22
+96 2089 22
+97 2111 22
+98 2133 22
+99 2155 22
+100 2177 22
+101 2199 22
+102 2221 22
+103 2243 22
+104 2265 22
+105 2287 22
+106 2309 20
+107 2329 22
+108 2351 22
+109 2373 22
+110 2395 22
+111 2417 22
+112 2439 20
+113 2459 20
+114 2479 22
+115 2501 22
+116 2523 20
+117 2543 20
+118 2563 22
+119 2585 21
+120 2606 22
+121 2628 20
+122 2648 20
+123 2668 22
+124 2690 22
+125 2712 20
+126 2732 20
+127 2752 22
+128 2774 24
+129 2798 20
+130 2818 22
+131 2840 22
+132 2862 24
+133 2886 20
+134 2906 22
+135 2928 22
+136 2950 24
+137 2974 20
+138 2994 22
+139 3016 22
+140 3038 24
+141 3062 20
+142 3082 22
+143 3104 20
+144 3124 24

data/stx_subtypes

diff -r 000000000000 -r 8be2feb96994 data/stx_subtypes

data/stx_subtypes

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data/stx_subtypes Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,147 @@
+stx1:1:M24352:1 stx1a
+stx1:3:M19437:3 stx1a
+stx1:4:L04539:4 stx1a
+stx1:5:Z36900:5 stx1a
+stx1:6:AB083044:6 stx1a
+stx1:7:AB035142:7 stx1a
+stx1:8:AM230663:8 stx1a
+stx1:9:AM230662:9 stx1a
+stx1:10:AJ279086:10 stx1a
+stx1:11:Z36899:11 stx1a
+stx1:12:AF461168:12 stx1a
+stx1:13:M19473:13 stx1a
+stx1:14:AB048232:14 stx1a
+stx1:15:AB071620:15 stx1a
+stx1:16:AB048237:16 stx1c
+stx1:17:AB071622:17 stx1c
+stx1:18:AB071624:18 stx1c
+stx1:19:DQ449666:19 stx1c
+stx1:20:Z36901:20 stx1c
+stx1:21:AB050958:21 stx1d
+stx1:22:AB050959:22 stx1d
+stx1:23:AY986980:23 stx1d
+stx1:24:AY170851:24 stx1d
+stx2:1:FM998851:1 stx2a
+stx2:2:AY443054:2 stx2a
+stx2:3:GQ429162:3 stx2a
+stx2:4:FM998852:4 stx2a
+stx2:5:GQ429163:5 stx2a
+stx2:6:GQ429168:6 stx2a
+stx2:7:FM998854:7 stx2a
+stx2:8:FM998861:8 stx2a
+stx2:9:FM998839:9 stx2a
+stx2:10:Z37725:10 stx2a
+stx2:11:FM998842:11 stx2a
+stx2:12:Z50754:12 stx2a
+stx2:13:AY443052:13 stx2a
+stx2:14:AJ272135:14 stx2a
+stx2:15:AF524944:15 stx2a
+stx2:16:FM998856:16 stx2a
+stx2:17:FM998858:17 stx2a
+stx2:18:EF441619:18 stx2a
+stx2:19:AY633459:19 stx2a
+stx2:20:GQ429170:20 stx2a
+stx2:21:AF461171:21 stx2a
+stx2:22:AY443057:22 stx2a
+stx2:23:AF461173:23 stx2a
+stx2:24:AB030484:24 stx2a
+stx2:25:AY633472:25 stx2a
+stx2:26:EF441613:26 stx2a
+stx2:27:AY633471:27 stx2a
+stx2:28:DQ344636:28 stx2a
+stx2:29:EF441609:29 stx2a
+stx2:30:EF441599:30 stx2a
+stx2:31:X07865:31 stx2a
+stx2:32:EF441618:32 stx2a
+stx2:33:EF441604:33 stx2c
+stx2:34:AY443044:34 stx2c
+stx2:35:L11079:35 stx2c
+stx2:36:M59432:36 stx2c
+stx2:37:FM177471:37 stx2c
+stx2:38:AF500189:38 stx2d
+stx2:39:AY443043:39 stx2c
+stx2:40:EU086525:40 stx2c
+stx2:41:AM982821:41 stx2c
+stx2:42:AY633464:42 stx2c
+stx2:43:AY633473:43 stx2c
+stx2:44:AY633453:44 stx2c
+stx2:45:AY633467:45 stx2c
+stx2:46:AY633469:46 stx2c
+stx2:47:AY739671:47 stx2c
+stx2:48:DQ235774:48 stx2c
+stx2:49:AB071845:49 stx2c
+stx2:50:AF461167:50 stx2c
+stx2:51:AF291819:51 stx2c
+stx2:52:AB015057:52 stx2c
+stx2:53:AY443045:53 stx2c
+stx2:54:AY633470:54 stx2c
+stx2:55:AY443049:55 stx2c
+stx2:56:FM998860:56 stx2c
+stx2:57:AY443047:57 stx2d
+stx2:58:AF479828:58 stx2d1
+stx2:59:GQ429172:59 stx2d
+stx2:60:AY633457:60 stx2d
+stx2:61:AY633458:61 stx2d
+stx2:62:AY443048:62 stx2d
+stx2:63:FM998848:63 stx2d
+stx2:64:AF500191:64 stx2d
+stx2:65:EF441621:65 stx2d
+stx2:66:FM99884:66 stx2d
+stx2:67:AF500190:67 stx2d
+stx2:68:DQ235775:68 stx2d
+stx2:69:AF479829:69 stx2d2
+stx2:70:AY739671:70 stx2d
+stx2:71:EU816447:71 stx2d
+stx2:72:X61283:72 stx2d
+stx2:73:EF441605:73 stx2d
+stx2:74:EF584538:74 stx2d
+stx2:75:AF329817:75 stx2d
+stx2:76:AF500192:76 stx2d
+stx2:77:AY095209:77 stx2d
+stx2:78:DQ059012:78 stx2d
+stx2:79:SNS:79 stx2d
+stx2:80:FN182287:80 stx2d
+stx2:81:FM998855:81 stx2d
+stx2:82:AB012102:82 stx2b
+stx2:83:AB048228:83 stx2b
+stx2:84:AB048238:84 stx2b
+stx2:85:AB048224:85 stx2b
+stx2:86:AB048223:86 stx2b
+stx2:87:AB048229:87 stx2b
+stx2:88:AB012101:88 stx2b
+stx2:89:AB048226:89 stx2b
+stx2:90:AB048225:90 stx2b
+stx2:91:AJ313015:91 stx2b
+stx2:92:AF043627:92 stx2b
+stx2:93:AJ567997:93 stx2b
+stx2:94:EF441616:94 stx2b
+stx2:95:AJ567995:95 stx2b
+stx2:96:L11078:96 stx2b
+stx2:97:X65949:97 stx2b
+stx2:98:AM904726:98 stx2e
+stx2:99:AB048227:99 stx2g
+stx2:100:AY286000:100 stx2g
+stx2:101:AB048236:101 stx2g
+stx2:102:AJ966783:102 stx2g
+stx2:103:AB472687:103 stx2f
+stx2:104:AJ010730:104 stx2f
+stx2:105:M29153:105 stx2f
+stx2:106:X81418:106 stx2e
+stx2:107:AJ313016:107 stx2e
+stx2:108:FM998844:108 stx2e
+stx2:109:U72191:109 stx2e
+stx2:110:M21534:110 stx2e
+stx2:111:X81417:111 stx2e
+stx2:112:X81415:112 stx2e
+stx2:113:X81416:113 stx2e
+stx2:114:FN182286:114 stx2e
+stx2:115:FM998846:115 stx2e
+stx2:116:AY368993:116 stx2e
+stx2:117:AM939642:117 stx2e
+stx2:118:FM998838:118 stx2e
+stx2:119:AY332411:119 stx2e
+stx2:120:AJ567998:120 stx2e
+stx2:121:AJ249351:121 stx2e
+stx2k:STEC309 stx2k
+stx2k:STEC388 stx2k
+stx2k:STEC409 stx2k
\ No newline at end of file

eurl_vtec_wgs_pt.xml

diff -r 000000000000 -r 8be2feb96994 eurl_vtec_wgs_pt.xml

EURL_VTEC_WGS_PT.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/eurl_vtec_wgs_pt.xml Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,212 @@
+<tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="3.2">
+    <description>performs various typing tools</description>
+    <requirements>
+        <requirement type="package" version="3.6">python</requirement>
+        <requirement type="package" version="5.26.2">perl</requirement>
+        <requirement type="package" version="1.7">perl-bioperl</requirement>
+        <requirement type="package" version="0.39">trimmomatic</requirement>
+        <requirement type="package" version="2.3.4">bowtie2</requirement>
+        <requirement type="package" version="1.3.1">samtools</requirement>
+        <requirement type="package" version="1.3.1">bcftools</requirement>
+        <requirement type="package" version="0.7.17">bwa</requirement>
+        <requirement type="package">mmseqs2</requirement>
+        <requirement type="package" version="3.14">spades</requirement>
+        <requirement type="package" version="2.3">skesa</requirement>
+        <requirement type="package" version="0.11.9">fastqc</requirement>
+        <requirement type="package" version="5.0.2">quast</requirement>
+        <requirement type="package" version="3.8">muscle</requirement>
+        <requirement type="package" version="2.16.1">mlst</requirement>
+        <requirement type="package" version="3.6.7">ncbi-amrfinderplus</requirement>
+        <requirement type="package" version="2020.2">tbb</requirement>
+    </requirements>
+    
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+    <command>
+<![CDATA[
+      python
+      $__tool_directory__/EURL_VTEC_WGS_PT.py --log $logfile --output $report_out --contigs $contigs --quast $quast --mlstsevenloci $mlstsevenloci
+      #if str( $library.type ) == "single":
+          -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
+          --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
+          --text1 $text_file_1
+      #elif str( $library.type ) == "paired":
+          -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
+          --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
+          --text1 $text_file_1
+          -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${library.input_2.name}'
+          --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path}
+          --text2 $text_file_2
+      #elif str( $library.type ) == "pairedcollection":
+          -1 ${library.input_pc.forward} --input1_ext ${library.input_pc.forward.ext} --input1_name '${library.input_pc.forward.name}'
+          --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
+          --text1 $text_file_1
+          -2 ${library.input_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.name}'
+          --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path}
+          --text2 $text_file_2
+      #end if
+      #if $serotyping:
+          --serotyping
+          --antigen_O $antigen_O --antigen_H $antigen_H
+      #end if
+      #if $virulotyping:
+          --virulotyping
+          --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id)
+      #end if
+      #if $shigatoxintyping:
+          --shigatoxintyping
+          --stx $stx
+      #end if
+      #if $amrtyping:
+          --amrtyping
+          --amr $amr
+          --amr_id $__app__.security.encode_id($amr..  <param name="type" value="single"/>
+            <param name="input_1" value="a_reads.fastq" ftype="fastqsanger"/>
+            <param name="serotyping" value="true"/>
+            <output name="report_out">
+                <assert_contents>
+                    <has_text text="wzx_208_AF529080_O26" />
+                    <has_text text="wzy_192_AF529080_O26" />
+                    <has_text text="fliC_269_AY337465_H11" />
+                    <has_text text="fliC_276_AY337472_H11" />
+                </assert_contents>
+            </output>
+            <output name="antigen_O" file="antigen_O" ftype="tabular" />
+            <output name="antigen_H" file="antigen_H" ftype="tabular" />
+        </test>
+    </tests>
+
+    <help>
+**EURL VTEC WGS PT Overview**
+This tool performs various typing tools:
+
+- Raw data quality check (FASTQC)
+
+- Trimming (Trimmomatic)
+
+- Assembly (SPAdes)
+
+- Virulotyping (patho_typing tool from the INNUENDO Project)
+
+- Multi Locus Sequence Typing (MLST 7 loci)
+
+- Serotyping (mmseqs2)
+
+- Shigatoxintyping (blastn of a consensus sequence against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU)
+
+- AMR typing (AMRFinderPlus)
+
+Istituto Superiore di Sanità
+
+European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
+
+Developer: Arnold Knijn arnold.knijn@iss.it
+
+The development of the Virulotyping tool has been supported by INNUENDO project (https://www.innuendoweb.org) co-funded by the European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2
+("New approaches in identifying and characterizing microbial and chemical hazards") and by the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - “Fundos Europeus Estruturais e de Investimento”
+from “Programa Operacional Regional Lisboa 2020” and by national funds from FCT - “Fundação para a Ciência e a Tecnologia” and BacGenTrack (TUBITAK/0004/2014)
+[FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)].
+    </help>
+    <citations>
+      <citation type="bibtex">@ARTICLE{andrews_s,
+            author = {Andrews, S},
+            keywords = {bioinformatics, ngs, qc},
+            title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
+            url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
+        }</citation>
+      <citation type="doi">10.1093/bioinformatics/btu170</citation>
+      <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
+      <citation type="doi">10.1038/nmeth.1923</citation>
+      <citation type="bibtex">@ARTICLE{seemann_t,
+            author = {Seemann, T},
+            keywords = {bioinformatics, ngs},
+            title = {{mlst}},
+            url = {https://github.com/tseemann/mlst/}
+        }</citation>
+      <citation type="doi">10.1089/cmb.2012.0021</citation>
+      <citation type="doi">10.1186/s13059-018-1540-z</citation>
+      <citation type="doi">10.1038/s41467-018-04964-5</citation>
+      <citation type="doi">10.1128/AAC.00483-19</citation>
+      <citation type="doi">10.1128/JCM.00008-15</citation>
+      <citation type="bibtex">@ARTICLE{andrews_s,
+            author = {Li, M, Copeland, A, and Han, J},
+            keywords = {bioinformatics, ngs},
+            title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}},
+            url = {https://www.osti.gov/servlets/purl/1016000/}
+        }</citation>
+      <citation type="bibtex">@ARTICLE{andrews_s,
+            author = {Edwards, RA},
+            keywords = {bioinformatics, ngs},
+            title = {{fastq-pair}},
+            url = {https://github.com/linsalrob/EdwardsLab/}
+        }</citation>
+      <citation type="doi">10.1186/1471-2105-10-421</citation>
+      <citation type="doi">10.1093/nar/gkh340</citation>
+    </citations>
+</tool>

report_head.html

diff -r 000000000000 -r 8be2feb96994 report_head.html

report_head.html

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/report_head.html Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,24 @@
+<!DOCTYPE html><html><head><title>EURL VTEC WGS PT summary report</title>
+  <style type="text/css">
+    body {font-family:"sans-serif","lucida Sans Unicode","Lucida Grande","Segoe UI";font-size:13px;}
+    h1 {font-weight:normal;font-size:2em;margin-top:0.3em;margin-bottom:0.3em;}
+    h4 {font-size:1.17em;margin-top:0;margin-bottom:0;}
+    .table-head td {border:1px solid #73ad21;border-radius:6px;}
+    .table-rep {border-collapse:collapse;font-size:13px;margin:auto;}
+    .table-rep th, .table-rep td {padding:5px 5px;}
+    .table-rep .title {caption-side:top;margin-top:12px;margin-bottom:6px;font-size:24px;text-align:left;}
+    .table-rep tbody td:last-child {border:0;}
+    .table-rep thead th:last-child {border:0; border-bottom: 1px solid #d7e1da;}
+    .table-rep thead th {border-right:1px solid #d7e1da;border-bottom:1px solid #d7e1da;}
+    .table-rep tbody td {color:#353535;border-right:1px solid #d7e1da;text-align:right;}
+    .table-rep tbody tr:nth-child(odd) td {background-color:#f4fff7;}
+    .table-rep tbody tr:nth-child(even) td {background-color:#e2e2e2;}
+    .table-cross tbody td {color:#353535;border-right:1px solid #d7e1da;text-align:right;}
+    .table-cross {border-collapse:collapse;font-size:13px;margin:auto;}
+    .table-cross th, .table-cross td {max-width:220px; word-wrap:break-word;}
+    .table-cross tr:nth-child(2n+1) {background: rgba(178, 178, 178, 0.5) none repeat scroll 0 0;}
+    .table-cross th:nth-child(2n), .table-cross td:nth-child(2n) {background: rgba(178, 178, 178, 0.5) none repeat scroll 0 0;}
+  </style> <meta charset='utf-8'>
+<body><div style="border: 1px solid #73ad21;max-width:940px;text-align:center;margin:auto;"></br>
+<table class="table table-head"><tr><td width="25%"><img src='https://aries.iss.it/static/images/aries.jpg' alt='ARIES' style='float:left;width:50%;padding-left:0.5cm;'>
+<img src='https://aries.iss.it/static/images/isseurlvtec.png' alt='ISS-EURL VTEC' style='float:left;width:30%'></td>

report_head2.html

diff -r 000000000000 -r 8be2feb96994 report_head2.html

report_head2.html

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/report_head2.html Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,2 @@
+<td style='width: 25%; padding-left: 0.2cm; text-align: left;'><h4>Istituto Superiore di Sanita</h4>
+Department of Food Safety, Nutrition and Veterinary Public Health<br/>European Union Reference Laboratory for <i>E. coli</i></td></tr></table>

report_tail.html

diff -r 000000000000 -r 8be2feb96994 report_tail.html

report_tail.html

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/report_tail.html Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,2 @@
+<br/></div></body></html>
+

scripts/.gitattributes

diff -r 000000000000 -r 8be2feb96994 scripts/.gitattributes

scripts/.gitattributes

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/.gitattributes Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,17 @@
+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Custom for Visual Studio
+*.cs     diff=csharp
+
+# Standard to msysgit
+*.doc diff=astextplain
+*.DOC diff=astextplain
+*.docx diff=astextplain
+*.DOCX diff=astextplain
+*.dot  diff=astextplain
+*.DOT  diff=astextplain
+*.pdf  diff=astextplain
+*.PDF diff=astextplain
+*.rtf diff=astextplain
+*.RTF diff=astextplain

scripts/.gitignore

diff -r 000000000000 -r 8be2feb96994 scripts/.gitignore

scripts/.gitignore

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/.gitignore Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,53 @@
+# mpmachado_stuff - file with different mpmachado stuffs
+mpmachado_stuff.*
+
+# Python stuff
+*.py[cod]
+
+# Windows image file caches
+Thumbs.db
+ehthumbs.db
+
+# Folder config file
+Desktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# =========================
+# Operating System Files
+# =========================
+
+# OSX
+# =========================
+
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk

scripts/GetConsensus.py

diff -r 000000000000 -r 8be2feb96994 scripts/GetConsensus.py

scripts/GetConsensus.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/GetConsensus.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,97 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+############################################################################
+# Istituto Superiore di Sanita'
+# European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
+# Developer: Arnold Knijn arnold.knijn@iss.it
+############################################################################
+"""
+
+import argparse
+import sys
+import os
+import subprocess
+import shutil
+
+def __main__():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--input', dest='input', help='input alignment file')
+    parser.add_argument('-o', '--output', dest='output', help='output consensus file')
+    args = parser.parse_args()
+
+    sequences = []
+    varsequences = []
+    # read input
+    with open(args.input) as alignments:
+        for alignment in alignments:
+            if alignment[0] != ">":
+                sequences.append(alignment.rstrip())
+    numsequences = len(sequences)
+    for j in range(0, numsequences + 1):
+        varsequences.append("")
+    lstnumvariants = []
+    lstnumhyphens = []
+    # loop over the columns
+    for i in range(0, len(sequences[0])):
+        variants = []
+        numhyphens = 0
+        # loop over the original rows to obtain variants
+        for j in range(0, numsequences):
+            if sequences[j][i:i+1] == "-":
+                numhyphens = numhyphens + 1
+            if sequences[j][i:i+1] not in variants and sequences[j][i:i+1] != "-":
+                variants.append(sequences[j][i:i+1])
+        lstnumvariants.append(len(variants))
+        lstnumhyphens.append(numhyphens)
+        # create varsequences with a template of the variants
+        for j in range(0, numsequences):
+            if lstnumhyphens[i] == 0:
+                varsequences[j] = varsequences[j] + "-"
+            elif lstnumvariants[i] < 2:
+                varsequences[j] = varsequences[j] + "-"
+            else:
+                varsequences[j] = varsequences[j] + sequences[j][i:i+1]
+        if lstnumvariants[i] == 1 and lstnumhyphens[i] > 0:
+            varsequences[numsequences] = varsequences[numsequences] + variants[0]
+        else:
+            varsequences[numsequences] = varsequences[numsequences] + "-"
+    # loop over the columns, apply single variant
+    for i in range(0, len(sequences[0])):
+        if lstnumvariants[i] == 1 and lstnumhyphens[i] > 0:
+            # loop over all the rows to apply single variant to "-"
+            for j in range(0, len(sequences)):
+                if sequences[j][i:i+1] == "-":
+                    lstsequence = list(sequences[j])
+                    lstsequence[i] = varsequences[numsequences][i:i+1]
+                    sequences[j] = ''.join(lstsequence)
+    # loop over the rows of the sequences, apply multiple variants
+    for j in range(0, len(sequences)):
+        # loop over the columns
+        for i in range(0, len(sequences[0])):
+            variants = []
+            if sequences[j][i:i+1] == "-" and lstnumvariants[i] > 1:
+                # loop over the rows of the varsequences
+                for k in range(0, numsequences):
+                    if varsequences[k][i:i+1] not in variants and varsequences[k][i:i+1] != "-":
+                        variants.append(varsequences[k][i:i+1])
+                        if len(variants) == 1:
+                            lstsequence = list(sequences[j])
+                            lstsequence[i] = variants[0]
+                            sequences[j] = ''.join(lstsequence)
+                        else:
+                            lstsequence[i] = variants[len(variants) - 1]
+                            sequences.append(''.join(lstsequence))
+    # eliminate duplicate sequences
+    sequences_unique = list(set(sequences))
+    # write consensus sequences to output
+    consensus = open(args.output, 'w')
+    n = 1
+    for sequence in sequences_unique:
+        consensus.write(">consensus_" + str(n) + "\n")
+        consensus.write(sequence + "\n")
+        n = n + 1
+
+
+if __name__ == "__main__":
+    __main__()
\ No newline at end of file

scripts/MultifastaFromBlast.pl

diff -r 000000000000 -r 8be2feb96994 scripts/MultifastaFromBlast.pl

scripts/MultifastaFromBlast.pl

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/MultifastaFromBlast.pl Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,44 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use English;
+
+# Parse arguments
+my ($inputs, $output) = @ARGV;
+# Run program
+unlink $output;
+my @infiles = split( /,/, $inputs );
+foreach(@infiles) {
+  transformFileContent($_, $output);
+}
+
+# read input file and write multifasta with sequence (forward or reverse complement)
+sub transformFileContent {
+  my ($infile, $outfile) = @_;
+  open my $if, '<', $infile or die "Cannot open : $infile!";
+  open my $of, '>>', $outfile or die "Cannot open : $outfile!";
+  my @lines = <$if>;
+  close $if;
+  foreach(@lines) {
+    my @elems = split( /\t/, $_ );
+    print $of ">$elems[0]\n";
+    chomp $elems[2];
+    if ($elems[1] == 1) {
+      print $of "$elems[2]\n";
+    }
+    else {
+   my $revcomp = reverseComplement($elems[2]);
+      print $of "$revcomp\n";
+    }
+  }
+  close $of;
+  return 0;
+}
+
+# calculate reverse complement
+sub reverseComplement {
+  my ($DNA) = @_;
+  my $revcom = reverse $DNA;
+  $revcom =~ tr/ACGTacgt/TGCAtgca/;
+  return $revcom;
+}

scripts/ReMatCh/.gitattributes

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/.gitattributes

scripts/ReMatCh/.gitattributes

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/.gitattributes Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,17 @@
+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Custom for Visual Studio
+*.cs     diff=csharp
+
+# Standard to msysgit
+*.doc diff=astextplain
+*.DOC diff=astextplain
+*.docx diff=astextplain
+*.DOCX diff=astextplain
+*.dot  diff=astextplain
+*.DOT  diff=astextplain
+*.pdf  diff=astextplain
+*.PDF diff=astextplain
+*.rtf diff=astextplain
+*.RTF diff=astextplain

scripts/ReMatCh/.gitignore

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/.gitignore

scripts/ReMatCh/.gitignore

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/.gitignore Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,53 @@
+# mpmachado_stuff - file with different mpmachado stuffs
+mpmachado_stuff.*
+
+# Python stuff
+*.py[cod]
+
+# Windows image file caches
+Thumbs.db
+ehthumbs.db
+
+# Folder config file
+Desktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# =========================
+# Operating System Files
+# =========================
+
+# OSX
+# =========================
+
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk

scripts/ReMatCh/__init__.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/__init__.py

scripts/ReMatCh/__init__.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/__init__.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,1 @@
+__version__ = '4.1.0'

scripts/ReMatCh/modules/checkMLST.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/modules/checkMLST.py

scripts/ReMatCh/modules/checkMLST.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/modules/checkMLST.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,216 @@
+import sys
+import os
+import urllib.request
+import csv
+from glob import glob
+import re
+import functools
+try:
+    import xml.etree.cElementTree as ET
+except ImportError:
+    import xml.etree.ElementTree as ET
+from . import utils
+from . import rematch_module
+
+
+def determine_species(species):
+    species = species.lower().split(' ')
+
+    if len(species) >= 2:
+        species = species[:2]
+        if species[1] in ('spp', 'spp.', 'complex'):
+            species = [species[0]]
+
+    return species
+
+
+def check_existing_schema(species, schema_number, script_path):
+    species = determine_species(species)
+
+    if schema_number is None:
+        schema_number = ''
+    else:
+        schema_number = '#' + str(schema_number)
+
+    mlst_schemas_folder = os.path.join(os.path.dirname(script_path), 'modules', 'mlst_schemas', '')
+    reference = []
+    files = [f for f in os.listdir(mlst_schemas_folder) if not f.startswith('.') and os.path.isfile(os.path.join(mlst_schemas_folder, f))]
+    for file_found in files:
+        file_path = os.path.join(mlst_schemas_folder, file_found)
+        if file_found.startswith('_'.join(species) + schema_number) and file_found.endswith('.fasta'):
+            reference = file_path
+
+    if len(reference) > 1:
+        if schema_number == '':
+            schema_number = '#1'
+        for scheme in reference:
+            if os.path.splitext(scheme)[0].endswith(schema_number):
+                reference = [scheme]
+                break
+    if len(reference) == 0:
+        reference = None
+    elif len(reference) == 1:
+        reference = reference[0]
+    return reference
+
+
+def write_mlst_reference(species, mlst_sequences, outdir, time_str):
+    print('Writing MLST alleles as reference_sequences' + '\n')
+    reference_file = os.path.join(outdir, str(species.replace('/', '_').replace(' ', '_') + '.' + time_str + '.fasta'))
+    with open(reference_file, 'wt') as writer:
+        for header, sequence in list(mlst_sequences.items()):
+            writer.write('>' + header + '\n')
+            fasta_sequence_lines = rematch_module.chunkstring(sequence, 80)
+            for line in fasta_sequence_lines:
+                writer.write(line + '\n')
+    return reference_file
+
+
+def get_st(mlst_dicts, dict_sequences):
+    SequenceDict = mlst_dicts[0]
+    STdict = mlst_dicts[1]
+    lociOrder = mlst_dicts[2]
+
+    alleles_profile = ['-'] * len(lociOrder)
+    for x, sequence_data in list(dict_sequences.items()):
+        if sequence_data['header'] not in SequenceDict:
+            print(sequence_data['header'] + ' not found between consensus sequences!')
+            break
+        if sequence_data['sequence'] in list(SequenceDict[sequence_data['header']].keys()):
+            allele_number = SequenceDict[sequence_data['header']][sequence_data['sequence']]
+            alleles_profile[lociOrder.index(sequence_data['header'])] = allele_number
+        else:
+            for sequence_st, allele_number in list(SequenceDict[sequence_data['header']].items()):
+                if sequence_st in sequence_data['sequence']:
+                    alleles_profile[lociOrder.index(sequence_data['header'])] = allele_number
+
+    alleles_profile = ','.join(alleles_profile)
+    st = '-'
+    if alleles_profile in STdict:
+        st = STdict[alleles_profile]
+
+    return st, alleles_profile
+
+
+downloadPubMLST = functools.partial(utils.timer, name='Download PubMLST module')
+
+
+@downloadPubMLST
+def download_pub_mlst_xml(originalSpecies, schema_number, outdir):
+    print('Searching MLST database for ' + originalSpecies)
+
+    xmlURL = 'http://pubmlst.org/data/dbases.xml'
+    try:
+        content = urllib.request.urlopen(xmlURL)
+        xml = content.read()
+        tree = ET.fromstring(xml)
+    except:
+        print("Ooops! There might be a ..cusInfo.text
+                                    loci[locusID.strip()] = locusUrl
+                                xmlData[scheme.text.strip()][retrieved].append(loci)
+    if success == 0:
+        sys.exit("\tError. No schema found for %s. Please refer to https://pubmlst.org/databases/" % (originalSpecies))
+    elif success > 1:
+        keys = list(xmlData.keys())
+        keys = sorted(keys)
+        print("\tWarning. More than one schema found for %s. only keeping the first"
+              " one... %s" % (originalSpecies, keys[0]))
+        for key in keys[1:]:
+            del xmlData[key]
+
+    pubmlst_dir = os.path.join(outdir, 'pubmlst', '')
+    if not os.path.isdir(pubmlst_dir):
+        os.makedirs(pubmlst_dir)
+
+    for SchemaName, info in list(xmlData.items()):
+        STdict = {}
+        SequenceDict = {}
+        mlst_sequences = {}
+
+        species_name = '_'.join(determine_species(SchemaName)).replace('/', '_')
+
+        for RetrievalDate, URL in list(info.items()):
+            schema_date = species_name + '_' + RetrievalDate
+            outDit = os.path.join(pubmlst_dir, schema_date)  # compatible with windows? See if it already exists, if so, break
+
+            if os.path.isdir(outDit):
+                pickle = os.path.join(outDit, str(schema_date + '.pkl'))
+                if os.path.isfile(pickle):
+                    print("\tschema files already exist for %s" % (SchemaName))
+                    mlst_dicts = utils.extract_variable_from_pickle(pickle)
+                    SequenceDict = mlst_dicts[0]
+                    for lociName, alleleSequences in list(SequenceDict.items()):
+                        for sequence in alleleSequences:
+                            if lociName not in list(mlst_sequences.keys()):
+                                mlst_sequences[lociName] = sequence
+                            else:
+                                break
+                    return mlst_dicts, mlst_sequences
+
+            elif any(species_name in x for x in os.listdir(pubmlst_dir)):
+                print("Older version of %s's scheme found! Deleting..." % (SchemaName))
+                for directory in glob(str(pubmlst_dir + str(species_name + '_*'))):
+                    utils.remove_directory(directory)
+                    os.makedirs(outDit)
+            else:
+                os.makedirs(outDit)
+
+            contentProfile = urllib.request.urlopen(URL[0])
+            header = next(contentProfile).decode("utf8").strip().split('\t')  # skip header
+            try:
+                indexCC = header.index('clonal_complex') if 'clonal_complex' in header else header.index('CC')
+            except:
+                indexCC = len(header)
+            lociOrder = header[1:indexCC]
+            for row in contentProfile:
+                row = row.decode("utf8").strip().split('\t')
+                ST = row[0]
+                alleles = ','.join(row[1:indexCC])
+                STdict[alleles] = ST
+            for lociName, lociURL in list(URL[1].items()):
+                if lociName not in list(SequenceDict.keys()):
+                    SequenceDict[lociName] = {}
+                url_file = os.path.join(outDit, lociURL.rsplit('/', 1)[1])
+                urllib.request.urlretrieve(lociURL, url_file)
+                sequences, ignore, ignore = rematch_module.get_sequence_information(url_file, 0)
+                for key in list(sequences.keys()):
+                    header = re.sub("\D", "", sequences[key]['header'])
+                    sequence = sequences[key]['sequence'].upper()
+                    SequenceDict[lociName][sequence] = header
+                    if lociName not in list(mlst_sequences.keys()):
+                        mlst_sequences[lociName] = sequence
+                os.remove(url_file)
+            mlst_dicts = [SequenceDict, STdict, lociOrder]
+            utils.save_variable_to_pickle(mlst_dicts, outDit, schema_date)
+    return mlst_dicts, mlst_sequences

scripts/ReMatCh/modules/download.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/modules/download.py

scripts/ReMatCh/modules/download.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/modules/download.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,599 @@
+import os.path
+import multiprocessing
+import sys
+import functools
+import time
+import subprocess
+
+try:
+    import modules.utils as utils
+except ImportError:
+    from ReMatCh.modules import utils as utils
+
+
+def get_read_run_info(ena_id):
+    import urllib.request
+
+    url = 'http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=' + ena_id + '&result=read_run'
+
+    read_run_info = None
+    try:
+        url = urllib.request.urlopen(url)
+        read_run_info = url.read().decode("utf8").splitlines()
+        if len(read_run_info) <= 1:
+            read_run_info = None
+    except Exception as error:
+        print(error)
+
+    return read_run_info
+
+
+def get_download_information(read_run_info):
+    header_line = read_run_info[0].split('\t')
+    info_line = read_run_info[1].split('\t')
+
+    download_information = {'fastq': None, 'submitted': None, 'cram_index': None}
+    download_types = ['aspera', 'ftp']
+
+    for i in range(0, len(header_line)):
+        header = header_line[i].lower().rsplit('_', 1)
+        if header[0] in list(download_information.keys()):
+            if header[1] in download_types:
+                if len(info_line[i]) > 0:
+                    files_path = info_line[i].split(';')
+                    if len(files_path) > 2:
+                        print('WARNING: Were found more files than expected in'
+                              ' {download_information}-{download_types} download'
+                              ' links!'.format(download_information=header[0], download_types=header[1]))
+                    if download_information[header[0]] is None:
+                        download_information[header[0]] = {}
+                    download_information[header[0]][header[1]] = files_path
+
+    return download_information
+
+
+def get_sequencing_information(read_run_info):
+    header_line = read_run_info[0].split('\t')
+    info_line = read_run_info[1].split('\t')
+
+    sequencing_information = {'run_accession': None, 'instrument_platform': None, 'instrument_model': None,
+                              'library_layout': None, 'library_source': None, 'extra_run_accession': None,
+                              'nominal_length': None, 'read_count': None, 'base_count': None,
+                              'date_download': time.strftime("%Y-%m-%d")}
+
+    for i in range(0, len(header_line)):
+        header = header_line[i].lower()
+        if header in list(sequencing_information.keys()):
+            if len(info_line[i]) > 0:
+                sequencing_information[header] = info_line[i]
+
+    if len(read_run_info) > 2:
+        extra_run_accession = []
+        for i in range(2, len(read_run_info)):
+            info = read_run_info[i].split('\t')
+            for j in range(0, len(header_line)):
+                header = header_line[j].lower()
+                if header == 'run_accession':
+                    if len(info[j]) > 0:
+                        extra_run_accession.append(info[j])
+        if len(extra_run_accession) >= 1:
+            sequencing_information['extra_run_accession'] = ','.join(extra_run_accession)
+
+    return sequencing_information
+
+
+@utils.trace_unhandled_exceptions
+def download_with_aspera(aspera_file_path, aspera_key, outdir, pickle_prefix, sra, ena_id):
+    command = ['ascp', '-QT', '-l', '300m', '', '-i', aspera_key, '', outdir]
+    if not sra:
+        command[4] = '-P33001'
+        command[7] = str('era-fasp@' + aspera_file_path)
+        pickle = pickle_prefix + '.' + aspera_file_path.rsplit('/', 1)[1]
+    else:
+        command[7] = 'anonftp@ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/{a}/{b}/{c}/{c}.sra'.format(
+            a=ena_id[:3], b=ena_id[:6], c=ena_id)
+        pickle = pickle_prefix + '.' + ena_id
+
+    run_successfully, stdout, stderr = utils.run_command_popen_com..oad': time.strftime("%Y-%m-%d")}
+
+    read_run_info = get_read_run_info(ena_id)
+    if read_run_info is not None:
+        download_information = get_download_information(read_run_info)
+        download_information = check_correct_links(download_information)
+        sequencing_information = get_sequencing_information(read_run_info)
+
+        if instrument_platform.lower() == 'all' or \
+                (sequencing_information['instrument_platform'] is not None and
+                 sequencing_information['instrument_platform'].lower() == instrument_platform.lower()):
+            if download_paired_type.lower() == 'both' or \
+                    (sequencing_information['library_layout'] is not None and
+                     sequencing_information['library_layout'].lower() == download_paired_type.lower()):
+                run_successfully, cram_index_run_successfully, download_sra = download_files(download_information,
+                                                                                             aspera_key, download_dir,
+                                                                                             download_cram_bam_true,
+                                                                                             sra, sra_opt, ena_id)
+                if download_sra:
+                    run_successfully = sra_2_fastq(download_dir, ena_id)
+                if run_successfully:
+                    run_successfully, downloaded_files = get_fastq_files(download_dir, cram_index_run_successfully,
+                                                                         threads,
+                                                                         sequencing_information['library_layout'])
+                if run_successfully and downloaded_files is not None:
+                    run_successfully, downloaded_files = rename_move_files(downloaded_files,
+                                                                           sequencing_information['run_accession'],
+                                                                           outdir,
+                                                                           sequencing_information['library_layout'])
+    else:
+        if sra or sra_opt:
+            run_successfully, cram_index_run_successfully, download_sra = download_files({'fastq': None,
+                                                                                          'submitted': None,
+                                                                                          'cram_index': None},
+                                                                                         aspera_key, download_dir,
+                                                                                         download_cram_bam_true, sra,
+                                                                                         sra_opt, ena_id)
+            if download_sra:
+                run_successfully = sra_2_fastq(download_dir, ena_id)
+            if run_successfully:
+                run_successfully, downloaded_files = get_fastq_files(download_dir, cram_index_run_successfully, threads,
+                                                                     'paired')
+                if not run_successfully:
+                    run_successfully, downloaded_files = get_fastq_files(download_dir, cram_index_run_successfully,
+                                                                         threads, 'single')
+            if run_successfully and downloaded_files is not None:
+                run_successfully, downloaded_files = rename_move_files(downloaded_files, ena_id, outdir, 'paired')
+                if not run_successfully:
+                    run_successfully, downloaded_files = rename_move_files(downloaded_files, ena_id, outdir, 'single')
+
+    utils.remove_directory(download_dir)
+
+    return run_successfully, downloaded_files, sequencing_information

scripts/ReMatCh/modules/mlst_schemas/escherichia_coli#1.fasta

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/modules/mlst_schemas/escherichia_coli#1.fasta

scripts/ReMatCh/modules/mlst_schemas/escherichia_coli#1.fasta

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/modules/mlst_schemas/escherichia_coli#1.fasta Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,87 @@
+>recA
+GTGGAAACCATCTCTACCGGTTCGCTTTCACTGGATATCGCGCTTGGGGCAGGTGGTCTGCCGATGGGCCGTATCGTCGA
+AATCTACGGACCGGAATCTTCCGGTAAAACCACGCTGACGCTGCAGGTGATCGCCGCAGCGCAGCGTGAAGGTAAAACCT
+GTGCGTTTATCGATGCTGAACACGCGCTGGACCCAATCTACGCACGTAAACTGGGCGTCGATATCGACAACCTGCTGTGC
+TCCCAGCCGGACACCGGCGAGCAGGCACTGGAAATCTGTGACGCCCTGGCGCGTTCTGGCGCAGTAGACGTTATCGTCGT
+TGACTCCGTGGCGGCACTGACGCCGAAAGCGGAAATCGAAGGCGAAATCGGCGACTCTCACATGGGCCTTGCGGCACGTA
+TGATGAGCCAGGCGATGCGTAAGCTGGCGGGTAACCTGAAGCAGTCCAACACGCTGCTGATCTTCATCAACCAGATCCGT
+ATGAAAATTGGTGTGATGTTCGGTAACCCGGAAACCACTACCGGTGGTAACGCGCTGAAATTCTACGCCTCTGTTCGTCT
+CGACATCCGTCGTATCGGCGCGGTGAAAGAGGGCGAAAACGTGGTGGGTAGCGAAACCCGCGTGAAAGTGGTGAAGAACA
+AAATCGCTGCGCCGTTTAAACAGGCTGAATTCCAGATCCTCTACGGCGAAGGTATCAACTTCTACGGCGAACTGGTTGAC
+CTGGGCGTAAAAGAGAAGCTGATCGAGAAAGCAGGCGCGTGGTACAGCTACAAAGGTGAGAAGATCGGTCAGGGTAAAGC
+GAATGCGACTGCCTGGCTGAAAGATAACCCGGAAACCGCGAAAGAGATCGAGAAGAAAGTACGTGAGTTGCTGCTGAGCA
+ACCCGAACTCAACGCCGGATTTCTCTGTAG
+>purA
+TGAAAAAACCGTTCTCCATCTTATTCCATCAGGTATTCTCCGCGAGAATGTAACCAGCATCATCGGTAACGGTGTTGTGC
+TGTCTCCGGCCGCGCTGATGAAAGAGATGAAAGAACTGGAAGACCGTGGCATCCCCGTTCGTGAGCGTCTGCTGCTGTCT
+GAAGCATGTCCGCTGATCCTTGATTATCACGTTGCGCTGGATAACGCGCGTGAGAAAGCGCGTGGCGCGAAAGCGATCGG
+CACCACCGGTCGTGGTATCGGGCCTGCTTATGAAGATAAAGTAGCACGTCGCGGTCTGCGTGTTGGCGACCTTTTCGACA
+AAGAAACCTTCGCTGAAAAACTGAAAGAAGTGATGGAATATCACAACTTCCAGTTGGTTAACTACTACAAAGCTGAAGCG
+GTTGATTACCAGAAAGTTCTGGATGATACGATGGCTGTTGCCGACATCCTGACTTCTATGGTGGTTGACGTTTCTGACCT
+GCTCGACCAGGCGCGTCAGCGTGGCGATTTCGTCATGTTTGAAGGTGCGCAGGGTACGCTGCTGGATATCGACCACGGTA
+CTTATCCGTACGTAACTTCTTCCAACACCACTGCTGGTGGCGTGGCGACCGGTTCCGGCCTGGGCCCGCGTTATGTTGAT
+TACGTTCTGGGTATCCTCAAAGCTTACTCCACTCGTGTAGGTGCAGGTCCGTTCCCGACCGAACTGTTTGATGAAACTGG
+CGAGTTCCTCTGCAAGCAGGGTAACGAATTCGGCGCAACTACGGGGCGTCGTCGTCGTACCGGCTGGCTGGACACCGTTG
+CCGTTCGTCGTGCGGTACAGCTGAACTCCCTGTCTGGCTTCTGCCTGACTAAACTGGACGTTCTGGATGGCCTGAAAG
+>mdh
+GTATTGGCCAGGCGCTTGCACTACTGTTAAAAACCCAACTGCCTTCAGGTTCAGAACTCTCTCTGTATGATATCGCTCCA
+GTGACTCCCGGTGTGGCTGTCGATCTGAGCCATATCCCTACTGCTGTGAAAATCAAAGGTTTTTCTGGTGAAGATGCGAC
+TCCGGCGCTGGAAGGCGCAGATGTCGTTCTTATCTCTGCAGGCGTAGCGCGTAAACCGGGTATGGATCGTTCCGACCTGT
+TTAACGTTAACGCCGGCATCGTGAAAAACCTGGTACAGCAAGTTGCGAAAACCTGCCCGAAAGCGTGCATTGGTATTATC
+ACTAACCCGGTTAACACCACAGTTGCAATTGCTGCTGAAGTGCTGAAAAAAGCCGGTGTTTATGACAAAAACAAACTGTT
+CGGCGTTACCACGCTGGATATCATTCGTTCCAACACCTTTGTTGCGGAACTGAAAGGCAAACAGCCAGGCGAAGTTGAAG
+TGCCGGTTATTGGCGGTCACTCTGGTGTTACCATTCTGCCGCTGCTGTCACAGGTTCCTGGCGTTAGTTTTACCGAGCAG
+GAAGTGGCTGATCTGACCAAACGCATCCAGAACGCGGGTACTGAAGTGGTTGAAGCGAAGGCCGGTGGCGGGTCTGCAAC
+CCTGTCTATGGGCCAGGCAGCTGCACGTTTTGGTCTGTCTCTGGTTCGTGCACTGCAGGGCGAACAAGGCGTTGTCGAAT
+GTGCCTACGTTGAAGGCGACGGTCAGTACGCCCGTTTCTTCTCTCAACCGCTGCTGCTGGGTAAAAACGGCGTGGAAGAG
+CGTAAATCTATCGGTACCCTGAGCGCATTTGAACAGAACGCGCTGGAAGGTA
+>icd
+CATATGCAACGTGGTGGCAGACGAGCAAACCAGTAGCGCTCGAAGGAGAGGTGAATGGAAAGTAAAGTAGTTGTTCCGGC
+ACAAGGCAAGAAGATCACCCTGCAAAACGGCAAACTCAACGTTCCTGAAAATCCGATTATCCCTTACATTGAAGGTGATG
+GAATCGGTGTAGATGTAACCCCAGCCATGCTGAAAGTGGTCGACGCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAA
+ATCTCCTGGATGGAAATTTACACCGGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCT
+TGATCTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTGGCGGTATTCGCTCTCTGAACG
+TTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCGGTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAA
+CACCCTGAACTGACCGATATGGTTATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTC
+TGCCGACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAAAATTCGCTTCCCGGAACATTGTGGTA
+TCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCTGGTTCGTGCAGCGATCGAATACGCAATTGCTAACGATCGT
+GACTCTGTGACTCTGGTGCACAAAGGCAACATCATGAAGTTCACCGAAGGAGCGTTTAAAGACTGGGGCTACCAGCTGGC
+GCGTGAAGAGTTTGGCGGTGAACTGATCGACGGTGGCCCGTGGCTGAAAGTTAAAAACCCGAACACTGGCAAAGAGATCG
+TCATTAAAGACGTGATTGCTGATGCATTCCTGCAACAG
+>gyrB
+CTATCGACGAAGCGCTCGCGGGTCACTGTAAAGAAATTATCGTCACCATTCACGCCGATAACTCTGTCTCTGTACAGGAT
+GACGGGCGCGGCATTCCGACCGGTATTCACCCGGAAGAGGGCGTATCGGCGGCGGAAGTGATCATGACCGTTCTGCACGC
+AGGCGGTAAATTTGACGATAACTCCTATAAAGTGTCCGGCGGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGT
+CGCAAAAACTGGAGCTGGTTATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCG
+CTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTCGAAACCTTCACCAATGTGAC
+CGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAGTTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCG
+ACAAGCGCGACGGCAAAGAAGACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAA
+ACGCCGATCCACCCGAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAAGTGGCGTTGCAGTGGAACGA
+TGGCTTCCAGGAAAACATCTACTGCTTTACCAACAACATTCCGCAGCGTGACGGCGGTACTCACCTGGCAGGCTTCCGTG
+CGGCGATGACCCGTACCCTGAACGCCTACATGGACAAAGAAGGCTACAGCAAAAAAGCCAAAGTCAGCGCCACCGGTGAC
+GATGCGCGTGAAGGCCTGATTGCGGTCGTTTCCGTGAAAGTGCCGGACCCGAAATTCTCC
+>fumC
+AGTACGCAGCGAAAAAGATTCGATGGGGGCGATTGATGTCCCGGCAGATAAGCTGTGGGGCGCACAAACTCAACGCTCGC
+TGGAGCATTTCCGCATTTCGACGGAGAAAATGCCCACCTCACTGATTCATGCGCTGGCGCTAACCAAGCGTGCAGCGGCA
+AAAGTTAATGAAGATTTAGGCTTGTTGTCTGAAGAGAAAGCGAGCGCCATTCGTCAGGCGGCGGATGAAGTACTGGCAGG
+ACAGCATGACGACGAATTCCCGCTGGCTATCTGGCAGACCGGCTCCGGCACGCAAAGTAACATGAACATGAACGAAGTGC
+TGGCTAACCGGGCCAGTGAATTACTCGGCGGTGTGCGCGGGATGGAACGTAAAGTTCACCCTAACGACGACGTGAACAAA
+AGCCAAAGTTCCAACGATGTCTTTCCGACGGCGATGCACGTTGCGGCGCTGCTGGCGCTGCGCAAGCAACTCATTCCTCA
+GCTTAAAACCCTGACACAGACACTGAATGAGAAATCCCGTGCTTTTGCCGATATCGTCAAAATTGGTCGTACTCACTTGC
+AGGATGCCACGCCGTTAACGCTGGGGCAGGAGATTTCCGGCTGGGTAGCGATGCTCGAGCATAATCTCAAACATATCGAA
+TACAGCCTGCCTCACGTAGCGGAACTGGCTCTTGGCGGTACAGCGGTGGGTACTGGACTAAATACCCATCCGGAGTATGC
+GCGTCGCGTAGCAGATGAACTGGCAGTCATTACCTGTGCACCGTTTGTTACCGCGCCGAACAAATTTGAAGCGCTGGCGA
+CCTGTGATGCCCTGGTTCAGGCGCACGGCGCGTTGAAAGGGTTGGCTGCGTCACTGATGAAAATCGCCA
+>adk
+TGACCTTCGTGTCATCCGGCATTTTTCTTTTCATCATCTGCACTTTCCGCAAATTATCTCGCCATTAACCGTTTCAGCCC
+CAGGTGCCTTTCTTGAGGCAATCGCCTGTTGGTGGTATCGTTTATCGCTTTTTCAAAAAATTCGACACATTTTAAGGGGA
+TTTTCGCAATGCGTATCATTCTGCTTGGCGCTCCGGGCGCGGGGAAAGGGACTCAGGCTCAGTTCATCATGGAGAAATAT
+GGTATTCCGCAAATCTCCACTGGCGATATGCTGCGTGCTGCGGTCAAATCTGGCTCCGAGCTGGGTAAACAAGCAAAAGA
+CATTATGGATGCTGGCAAACTGGTCACCGACGAACTGGTGATCGCGCTGGTTAAAGAGCGCATTGCTCAGGAAGACTGCC
+GTAATGGTTTCCTGTTGGACGGCTTCCCGCGTACCATTCCGCAGGCAGACGCGATGAAAGAAGCGGGCATCAATGTTGAT
+TACGTTCTGGAATTCGACGTACCGGACGAACTGATCGTTGACCGTATCGTCGGTCGCCGCGTTCATGCGCCGTCTGGTCG
+TGTTTATCACGTTAAATTCAATCCGCCGAAAGTAGAAGGCAAAGACGACGTTACCGGTGAAGAACTGACTACCCGTAAAG
+ATGATCAGGAAGAGACCGTACGTAAACGTCTGGTTGAATACCATCAGATGACAGCACCGCTGATCGGCTACTACTCCAAA
+GAAGCAGAAGCGGGTAATACCAAATACGCGAAAGTTGACGGCACCAAGCCGGTTGCTGAAGTTCGCGCTGATCTGGAAAA
+AATCCTCGGCTAATTCGAAAGCGCGCACGGACAGTCCCCTCGCCCCCTCGGGGAGAGGGTTAGGGTGAGGGGAACAGGCC
+CGCACAAGCAAACTTATCAGCAATCTCAGGCCGGATATTCATTCGGCCTTTTACAA

scripts/ReMatCh/modules/rematch_module.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/modules/rematch_module.py

scripts/ReMatCh/modules/rematch_module.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/modules/rematch_module.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,1255 @@
+import os.path
+import multiprocessing
+import functools
+import sys
+import pickle
+
+# https://chrisyeh96.github.io/2017/08/08/definitive-guide-python-imports.html#case-2-syspath-could-change
+sys.path.insert(0, os.path.dirname(os.path.realpath(__file__)))
+import utils
+
+
+def index_fasta_samtools(fasta, region_none, region_outfile_none, print_comand_true):
+    command = ['samtools', 'faidx', fasta, '', '', '']
+    shell_true = False
+    if region_none is not None:
+        command[3] = region_none
+    if region_outfile_none is not None:
+        command[4] = '>'
+        command[5] = region_outfile_none
+        shell_true = True
+    run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, shell_true, None, print_comand_true)
+    return run_successfully, stdout
+
+
+# Indexing reference file using Bowtie2
+def index_sequence_bowtie2(reference_file, threads):
+    if os.path.isfile(str(reference_file + '.1.bt2')):
+        run_successfully = True
+    else:
+        command = ['bowtie2-build', '--threads', str(threads), reference_file, reference_file]
+        run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, True)
+    return run_successfully
+
+
+# Mapping with Bowtie2
+def mapping_bowtie2(fastq_files, reference_file, threads, outdir, num_map_loc,
+                    bowtie_algorithm='--very-sensitive-local', bowtie_opt=None):
+    sam_file = os.path.join(outdir, str('alignment.sam'))
+
+    # Index reference file
+    run_successfully = index_sequence_bowtie2(reference_file, threads)
+
+    if run_successfully:
+        command = ['bowtie2', '', '', '-q', bowtie_algorithm, '--threads', str(threads), '-x',
+                   reference_file, '', '--no-unal', '', '-S', sam_file]
+
+        if num_map_loc is not None and num_map_loc > 1:
+            command[1] = '-k'
+            command[2] = str(num_map_loc)
+
+        if len(fastq_files) == 1:
+            command[9] = '-U ' + fastq_files[0]
+        elif len(fastq_files) == 2:
+            command[9] = '-1 ' + fastq_files[0] + ' -2 ' + fastq_files[1]
+        else:
+            return False, None
+
+        if bowtie_opt is not None:
+            command[11] = bowtie_opt
+
+        run_successfully, stdout, stderr = utils.run_command_popen_communicate(command, False, None, True)
+
+    if not run_successfully:
+        sam_file = None
+
+    return run_successfully, sam_file
+
+
+def split_cigar(cigar):
+    cigars = ['M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X']
+
+    splited_cigars = []
+    numbers = ''
+    for char in cigar:
+        if char not in cigars:
+            numbers += char
+        else:
+            splited_cigars.append([int(numbers), char])
+            numbers = ''
+
+    return splited_cigars
+
+
+def recode_cigar_based_on_base_quality(cigar, bases_quality, soft_clip_base_quality, mapping_position,
+                                       direct_strand_true, soft_clip_cigar_flag_recode):
+    cigar = split_cigar(cigar)
+    soft_left = []
+    soft_right = []
+    cigar_flags_for_reads_length = ('M', 'I', 'S', '=', 'X')
+    read_length_without_right_s = sum([cigar_part[0] for cigar_part in cigar if
+                                       cigar_part[1] in cigar_flags_for_reads_length]) - \
+                                  (cigar[len(cigar) - 1][0] if cigar[len(cigar) - 1][1] == 'S' else 0)
+    for x, base in enumerate(bases_quality):
+        if ord(base) - 33 >= soft_clip_base_quality:
+            if x <= cigar[0][0] - 1:
+                if cigar[0][1] == 'S':
+                    soft_left.append(x)
+            elif x > read_length_without_right_s - 1:
+                if cigar[len(cigar) - 1][1] == 'S':
+                    soft_right.append(x)
+
+    left_changed = (False, 0)
+    if len(soft_left) > 0:
+        soft_left = ..int('Analysing alignment data')
+            run_successfully, sample_data, consensus_files, consensus_sequences = \
+                sequence_data(sample, reference_file, bam_file, rematch_folder, threads, length_extra_seq,
+                              minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele,
+                              debug_mode_true, not_write_consensus)
+
+            if run_successfully:
+                print('Writing report file')
+                number_absent_genes = 0
+                number_genes_multiple_alleles = 0
+                mean_sample_coverage = 0
+                with open(os.path.join(outdir, 'rematchModule_report.txt'), 'wt') as writer:
+                    print('\n'.join(outdir, 'rematchModule_report.txt'))
+                    writer.write('\t'.join(['#gene', 'percentage_gene_coverage', 'gene_mean_read_coverage',
+                                            'percentage_gene_low_coverage', 'number_positions_multiple_alleles',
+                                            'percentage_gene_identity']) + '\n')
+                    for i in range(1, len(sample_data) + 1):
+                        writer.write('\t'.join([gene_list_reference[sample_data[i]['header']],
+                                                str(round(sample_data[i]['gene_coverage'], 2)),
+                                                str(round(sample_data[i]['gene_mean_read_coverage'], 2)),
+                                                str(round(sample_data[i]['gene_low_coverage'], 2)),
+                                                str(sample_data[i]['gene_number_positions_multiple_alleles']),
+                                                str(round(sample_data[i]['gene_identity'], 2))]) + '\n')
+
+                        if sample_data[i]['gene_coverage'] < minimum_gene_coverage or \
+                                sample_data[i]['gene_identity'] < minimum_gene_identity:
+                            number_absent_genes += 1
+                        else:
+                            mean_sample_coverage += sample_data[i]['gene_mean_read_coverage']
+                            if sample_data[i]['gene_number_positions_multiple_alleles'] > 0:
+                                number_genes_multiple_alleles += 1
+
+                    if len(sample_data) - number_absent_genes > 0:
+                        mean_sample_coverage = \
+                            float(mean_sample_coverage) / float(len(sample_data) - number_absent_genes)
+                    else:
+                        mean_sample_coverage = 0
+
+                    writer.write('\n'.join(['#general',
+                                            '>number_absent_genes', str(number_absent_genes),
+                                            '>number_genes_multiple_alleles', str(number_genes_multiple_alleles),
+                                            '>mean_sample_coverage', str(round(mean_sample_coverage, 2))]) + '\n')
+
+                    print('\n'.join([str('number_absent_genes: ' + str(number_absent_genes)),
+                                     str('number_genes_multiple_alleles: ' + str(number_genes_multiple_alleles)),
+                                     str('mean_sample_coverage: ' + str(round(mean_sample_coverage, 2)))]))
+
+    if not debug_mode_true:
+        utils.remove_directory(rematch_folder)
+
+    return run_successfully, sample_data if 'sample_data' in locals() else None, \
+           {'number_absent_genes': number_absent_genes if 'number_absent_genes' in locals() else None,
+            'number_genes_multiple_alleles': number_genes_multiple_alleles if
+            'number_genes_multiple_alleles' in locals() else None,
+            'mean_sample_coverage': round(mean_sample_coverage, 2) if 'mean_sample_coverage' in locals() else None}, \
+           consensus_files if 'consensus_files' in locals() else None,\
+           consensus_sequences if 'consensus_sequences' in locals() else None

scripts/ReMatCh/modules/seqFromWebTaxon.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/modules/seqFromWebTaxon.py

scripts/ReMatCh/modules/seqFromWebTaxon.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/modules/seqFromWebTaxon.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,146 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+'''
+Adapted from:
+https://github.com/mickaelsilva/pythonscripts/blob/master/SeqOfWeb/SeqFromWebTaxon.py
+mickaelsilva
+'''
+
+import sys
+import urllib.request
+import urllib.parse
+import xml.etree.ElementTree as ET
+import time
+import argparse
+import os
+
+
+def run_seq_from_web_taxon(taxonname, outputfile, getmachine, getOmicsDataType, getLibraryType, print_True):
+    print('\n' + 'Searching RunIDs for ' + taxonname)
+
+    taxonname = urllib.parse.quote(taxonname)
+    url = "http://www.ebi.ac.uk/ena/data/view/Taxon%3A" + taxonname + "&display=xml"
+    try:
+        content = urllib.request.urlopen(url)
+        xml = content.read()
+        tree = ET.fromstring(xml)
+        taxonid = ''
+    except:
+        print("Ooops!There might be a problem with the ena service, try later or check if the xml is well formated"
+              " at " + url)
+        raise
+    for child in tree:
+        taxonid = child.get('taxId')
+    if (taxonid):
+        print("\n" + "Taxon ID found: " + taxonid)
+        url = "http://www.ebi.ac.uk/ena/data/warehouse/search?query=%22tax_tree%28" + \
+              taxonid + \
+              "%29%22&result=read_run&display=xml"
+
+        content = urllib.request.urlopen(url)
+        xml = content.read()
+        tree = ET.fromstring(xml)
+
+        runid = ''
+        n = 0
+        with open(outputfile, "wt") as f:
+            f.write('#' + str(time.strftime("%d/%m/%Y")) + "\n")
+            model = ''
+            prjid = ''
+            length_line = 0
+            omics = ''
+            libraryType = ''
+            for child in tree:
+                runid = child.get('accession')
+
+                n += 1
+
+                if getmachine is True or getOmicsDataType is True or getLibraryType is True:
+                    for child2 in child:
+                        if child2.tag == 'EXPERIMENT_REF':
+                            expid = child2.get('accession')
+                            url2 = "http://www.ebi.ac.uk/ena/data/view/" + expid + "&display=xml"
+                            content = urllib.request.urlopen(url2)
+                            xml = content.read()
+                            tree2 = ET.fromstring(xml)
+                            try:
+                                for child3 in tree2:
+                                    for child4 in child3:
+                                        if child4.tag == 'PLATFORM':
+                                            for child5 in child4:
+                                                for child6 in child5:
+                                                    if child6.tag == 'INSTRUMENT_MODEL':
+                                                        model = child6.text
+                                        elif child4.tag == 'STUDY_REF':
+                                            prjid = child4.get('accession')
+                                        elif child4.tag == 'DESIGN':
+                                            if getOmicsDataType is True or getLibraryType is True:
+                                                for child5 in child4:
+                                                    if child5.tag == 'LIBRARY_DESCRIPTOR':
+                                                        for child6 in child5:
+                                                            if child6.tag == 'LIBRARY_SOURCE' and getOmicsDataType is True:
+                                                                omics = child6.text
+                                                            elif child6.tag == 'LIBRARY_LAYOUT' and getLibraryType is True:
+                                                                libraryType = child6[0].tag
+                            except:
+                                model = 'not found'
+                                omics = 'not found'
+                                libraryType = 'not found'
+                    f.write(str(runid) + "\t" + model + "\t" + prjid + "\t" + omics + "\t" + libraryType + "\n")
+                    if print_True:
+                        line = "run acession %s sequenced on %s from project %s for %s %s end" \
+                               " data" % (runid, model, prjid, omics, libraryType)
+                        if length_line < len(line):
+                            length_line = len(line)
+                        sys.stderr.write("\r" + line + str(' ' * (length_line - len(line))))
+                        sys.stderr.flush()
+                else:
+                    f.write(str(runid) + '\t' * 4 + "\n")
+                    if print_True:
+                        line = "run acession %s" % (runid, prjid)
+                        if length_line < len(line):
+                            length_line = len(line)
+                        sys.stderr.write("\r" + line + str(' ' * (length_line - len(line))))
+                        sys.stderr.flush()
+        print("\n")
+        print("\n"
+              "found %s run id's" % n)
+
+    else:
+        print("taxon name does not exist")
+
+
+def main():
+    parser = argparse.ArgumentParser(description="This program gets a list of sequencing runs and machine were the"
+                                                 " sequencing was performed, given a taxon name accepted by the"
+                                                 " European nucleotide Archive")
+    parser.add_argument('-i', nargs=1, type=str, help='taxon name', metavar='"Streptococcus agalactiae"', required=True)
+    parser.add_argument('-o', nargs=1, type=str, help='output file name', required=True)
+    parser.add_argument('-g', help='True to include sequencing machine in the output', action='store_true',
+                        required=False)
+    parser.add_argument('--getOmicsDataType', help='Informs the programme to include OMICS data type'
+                                                   ' (examples: GENOMIC / TRANSCRIPTOMIC / SYNTHETIC) in the output',
+                        action='store_true')
+    parser.add_argument('--getLibraryType', help='Informs the programme to include library type'
+                                                 ' (examples: PAIRED / SINGLE) in the output', action='store_true')
+
+    args = parser.parse_args()
+
+    getmachine = args.g
+    taxonname = args.i[0]
+
+    outdir = os.path.dirname(os.path.abspath(args.o[0]))
+    if not os.path.isdir(outdir):
+        os.makedirs(outdir)
+    outputfile = os.path.abspath(args.o[0])
+
+    getOmicsDataType = args.getOmicsDataType
+    getLibraryType = args.getLibraryType
+
+    run_seq_from_web_taxon(taxonname, outputfile, getmachine, getOmicsDataType, getLibraryType, True)
+
+
+if __name__ == "__main__":
+    main()

scripts/ReMatCh/modules/utils.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/modules/utils.py

scripts/ReMatCh/modules/utils.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/modules/utils.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,333 @@
+import pickle
+from traceback import format_exception as traceback_format_exception
+import shlex
+import subprocess
+from threading import Timer
+import shutil
+import time
+from functools import wraps as functools_wraps
+import os.path
+import sys
+
+
+def start_logger(workdir):
+    time_str = time.strftime("%Y%m%d-%H%M%S")
+    sys.stdout = Logger(workdir, time_str)
+    logfile = sys.stdout.getLogFile()
+    return logfile, time_str
+
+
+class Logger(object):
+    def __init__(self, out_directory, time_str):
+        self.logfile = os.path.join(out_directory, str('run.' + time_str + '.log'))
+        self.terminal = sys.stdout
+        self.log = open(self.logfile, "w")
+
+    def write(self, message):
+        self.terminal.write(message)
+        self.log.write(message)
+        self.log.flush()
+
+    def flush(self):
+        pass
+
+    def getLogFile(self):
+        return self.logfile
+
+
+def get_cpu_information(outdir, time_str):
+    with open(os.path.join(outdir, 'cpu_information.' + time_str + '.cpu.txt'), 'wt') as writer:
+        command = ['cat', '/proc/cpuinfo']
+        run_successfully, stdout, stderr = run_command_popen_communicate(command, False, None, False)
+        if run_successfully:
+            writer.write(stdout)
+
+    with open(os.path.join(outdir, 'cpu_information.' + time_str + '.slurm.txt'), 'wt') as writer:
+        for environment in sorted(os.environ):
+            if environment.startswith('SLURM_'):
+                writer.write('#' + environment + '\n' + os.environ[environment] + '\n')
+
+
+def setPATHvariable(doNotUseProvidedSoftware, script_path):
+    path_variable = os.environ['PATH']
+    script_folder = os.path.dirname(script_path)
+    # Set path to use provided softwares
+    if not doNotUseProvidedSoftware:
+        bowtie2 = os.path.join(script_folder, 'src', 'bowtie2-2.2.9')
+        samtools = os.path.join(script_folder, 'src', 'samtools-1.3.1', 'bin')
+        bcftools = os.path.join(script_folder, 'src', 'bcftools-1.3.1', 'bin')
+
+        os.environ['PATH'] = str(':'.join([bowtie2, samtools, bcftools, path_variable]))
+
+    # Print PATH variable
+    print('\n' + 'PATH variable:')
+    print(os.environ['PATH'])
+
+
+def checkPrograms(programs_version_dictionary):
+    print('\n' + 'Checking dependencies...')
+    programs = programs_version_dictionary
+    which_program = ['which', '']
+    listMissings = []
+    for program in programs:
+        which_program[1] = program
+        run_successfully, stdout, stderr = run_command_popen_communicate(which_program, False, None, False)
+        if not run_successfully:
+            listMissings.append(program + ' not found in PATH.')
+        else:
+            print(stdout.splitlines()[0])
+            if programs[program][0] is None:
+                print(program + ' (impossible to determine programme version) found at: ' + stdout.splitlines()[0])
+            else:
+                if program.endswith('.jar'):
+                    check_version = ['java', '-jar', stdout.splitlines()[0], programs[program][0]]
+                    programs[program].append(stdout.splitlines()[0])
+                else:
+                    check_version = [stdout.splitlines()[0], programs[program][0]]
+                run_successfully, stdout, stderr = run_command_popen_communicate(check_version, False, None, False)
+                if stdout == '':
+                    stdout = stderr
+                if program in ['wget', 'awk']:
+                    version_line = stdout.splitlines()[0].split(' ', 3)[2]
+                elif program in ['prefetch', 'fastq-dump']:
+                    version_line = stdout.splitlines()[1].split(' ')[-1]
+                else:
+                    version_line = stdout.splitlines()[0].split(' ')[-1]
+                replace_characters = ['"', 'v', 'V', '+', ',']
+       ..ate(command, False, 15, False)
+            print(stdout)
+        except:
+            print('HARMLESS WARNING: git command possibly not found. The GitHub repository information will not be'
+                  ' obtained.')
+        finally:
+            os.chdir(current_directory)
+
+
+def run_time(start_time):
+    end_time = time.time()
+    time_taken = end_time - start_time
+    hours, rest = divmod(time_taken, 3600)
+    minutes, seconds = divmod(rest, 60)
+    print('Runtime :' + str(hours) + 'h:' + str(minutes) + 'm:' + str(round(seconds, 2)) + 's')
+    return round(time_taken, 2)
+
+
+def timer(function, name):
+    @functools_wraps(function)
+    def wrapper(*args, **kwargs):
+        print('\n' + 'RUNNING {0}\n'.format(name))
+        start_time = time.time()
+
+        results = list(function(*args, **kwargs))  # guarantees return is a list to allow .insert()
+
+        time_taken = run_time(start_time)
+        print('END {0}'.format(name))
+
+        results.insert(0, time_taken)
+        return results
+    return wrapper
+
+
+def remove_directory(directory):
+    if os.path.isdir(directory):
+        shutil.rmtree(directory)
+
+
+def save_variable_to_pickle(variableToStore, outdir, prefix):
+    pickleFile = os.path.join(outdir, str(prefix + '.pkl'))
+    with open(pickleFile, 'wb') as writer:
+        pickle.dump(variableToStore, writer)
+
+
+def extract_variable_from_pickle(pickleFile):
+    with open(pickleFile, 'rb') as reader:
+        variable = pickle.load(reader)
+    return variable
+
+
+def trace_unhandled_exceptions(func):
+    @functools_wraps(func)
+    def wrapped_func(*args, **kwargs):
+        try:
+            func(*args, **kwargs)
+        except Exception as e:
+            print('Exception in ' + func.__name__)
+            print(e)
+
+            exc_type, exc_value, exc_tb = sys.exc_info()
+            print(''.join(traceback_format_exception(exc_type, exc_value, exc_tb)))
+
+            raise exc_type(exc_value)
+
+    return wrapped_func
+
+
+def kill_subprocess_Popen(subprocess_Popen, command):
+    print('Command run out of time: ' + str(command))
+    subprocess_Popen.kill()
+
+
+def run_command_popen_communicate(command, shell_True, timeout_sec_None, print_comand_True):
+    run_successfully = False
+    if not isinstance(command, str):
+        command = ' '.join(command)
+    command = shlex.split(command)
+
+    if print_comand_True:
+        print('Running: ' + ' '.join(command))
+
+    if shell_True:
+        command = ' '.join(command)
+        proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
+    else:
+        proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+    not_killed_by_timer = True
+    if timeout_sec_None is None:
+        stdout, stderr = proc.communicate()
+    else:
+        time_counter = Timer(timeout_sec_None, kill_subprocess_Popen, args=(proc, command,))
+        time_counter.start()
+        stdout, stderr = proc.communicate()
+        time_counter.cancel()
+        not_killed_by_timer = time_counter.isAlive()
+
+    if proc.returncode == 0:
+        run_successfully = True
+    else:
+        if not print_comand_True and not_killed_by_timer:
+            print('Running: ' + str(command))
+        if len(stdout) > 0:
+            print('STDOUT')
+            print(stdout.decode("utf-8"))
+        if len(stderr) > 0:
+            print('STDERR')
+            print(stderr.decode("utf-8"))
+    return run_successfully, stdout.decode("utf-8"), stderr.decode("utf-8")
+
+
+def rchop(string, ending):
+    if string.endswith(ending):
+        string = string[:-len(ending)]
+    return string
+
+
+def reverse_complement(seq):
+    complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N'}
+
+    reverse_complement_string = ''
+
+    seq = reversed(list(seq.upper()))
+
+    for base in seq:
+        reverse_complement_string += complement[base]
+
+    return reverse_complement_string

scripts/ReMatCh/rematch.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/rematch.py

scripts/ReMatCh/rematch.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/rematch.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,746 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+"""
+rematch.py - Reads mapping against target sequences, checking mapping
+and consensus sequences production
+<https://github.com/B-UMMI/ReMatCh/>
+
+Copyright (C) 2019 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+
+Last modified: August 08, 2019
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import os
+import sys
+import time
+import argparse
+
+try:
+    from __init__ import __version__
+
+    import modules.utils as utils
+    import modules.seqFromWebTaxon as seq_from_web_taxon
+    import modules.download as download
+    import modules.rematch_module as rematch_module
+    import modules.checkMLST as check_mlst
+except ImportError:
+    from ReMatCh.__init__ import __version__
+
+    from ReMatCh.modules import utils as utils
+    from ReMatCh.modules import seqFromWebTaxon as seq_from_web_taxon
+    from ReMatCh.modules import download as download
+    from ReMatCh.modules import rematch_module as rematch_module
+    from ReMatCh.modules import checkMLST as check_mlst
+
+
+def search_fastq_files(directory):
+    files_extensions = ['.fastq.gz', '.fq.gz']
+    pair_end_files_separation = [['_R1_001.f', '_R2_001.f'], ['_1.f', '_2.f']]
+
+    list_ids = {}
+    directories = [d for d in os.listdir(directory) if
+                   not d.startswith('.') and os.path.isdir(os.path.join(directory, d, ''))]
+    for directory_found in directories:
+        if directory_found != 'pubmlst':
+            directory_path = os.path.join(directory, directory_found, '')
+
+            fastq_found = []
+            files = [f for f in os.listdir(directory_path) if
+                     not f.startswith('.') and os.path.isfile(os.path.join(directory_path, f))]
+            for file_found in files:
+                if file_found.endswith(tuple(files_extensions)):
+                    fastq_found.append(file_found)
+
+            if len(fastq_found) == 1:
+                list_ids[directory_found] = [os.path.join(directory_path, f) for f in fastq_found]
+            elif len(fastq_found) >= 2:
+                file_pair = []
+
+                # Search pairs
+                for pe_separation in pair_end_files_separation:
+                    for fastq in fastq_found:
+                        if pe_separation[0] in fastq or pe_separation[1] in fastq:
+                            file_pair.append(fastq)
+
+                    if len(file_pair) == 2:
+                        break
+                    else:
+                        file_pair = []
+
+                # Search single
+                if len(file_pair) == 0:
+                    for pe_separation in pair_end_files_separation:
+                        for fastq in fastq_found:
+                            if pe_separation[0] not in fastq or pe_separation[1] not in fastq:
+                                file_pair.append(fastq)
+
+                    if len(file_pair) >= 1:
+                        file_pair = file_pair[0]
+
+                if len(file_pair) >= 1:
+                    list_ids[directory_found] = [os.path.join(directory_path, f) for f in file_pair]
+
+    return list_ids
+
+
+def get_list_ids_from_file(file_list_ids):
+    list_ids = []
+
+    with open(file_list_ids, 'rtU') as lines:
+        for line in..InstrumentPlatform', type=str, metavar='ILLUMINA',
+                                          help='Tells ReMatCh to download files with specific library layout (available'
+                                               ' options: %(choices)s)', choices=['ILLUMINA', 'ALL'], required=False,
+                                          default='ILLUMINA')
+    parser_optional_download.add_argument('--downloadCramBam', action='store_true',
+                                          help='Tells ReMatCh to also download cram/bam files and convert them to fastq'
+                                               ' files')
+
+    parser_optional_sra = parser.add_mutually_exclusive_group()
+    parser_optional_sra.add_argument('--SRA', action='store_true',
+                                     help='Tells getSeqENA.py to download reads in fastq format only from NCBI SRA'
+                                          ' database (not recommended)')
+    parser_optional_sra.add_argument('--SRAopt', action='store_true',
+                                     help='Tells getSeqENA.py to download reads from NCBI SRA if the download from ENA'
+                                          ' fails')
+
+    parser_optional_soft_clip = parser.add_argument_group('Soft clip facultative options')
+    parser_optional_soft_clip.add_argument('--softClip_baseQuality', type=int, metavar='N',
+                                           help='Base quality phred score in reads soft clipped regions',
+                                           required=False,
+                                           default=7)
+    parser_optional_soft_clip.add_argument('--softClip_recodeRun', type=str, metavar='first',
+                                           help='ReMatCh run to recode soft clipped regions (available'
+                                                ' options: %(choices)s)', choices=['first', 'second', 'both', 'none'],
+                                           required=False, default='none')
+    parser_optional_soft_clip.add_argument('--softClip_cigarFlagRecode', type=str, metavar='M',
+                                           help='CIGAR flag to recode CIGAR soft clip (available options: %(choices)s)',
+                                           choices=['M', 'I', 'X'], required=False, default='X')
+
+    args = parser.parse_args()
+
+    msg = []
+    if args.reference is None and not args.mlstReference:
+        msg.append('At least --reference or --mlstReference should be provided')
+    elif args.reference is not None and args.mlstReference:
+        msg.append('Only --reference or --mlstReference should be provided')
+    else:
+        if args.mlstReference:
+            if args.mlst is None:
+                msg.append('Please provide species name using --mlst')
+    if args.minFrequencyDominantAllele < 0 or args.minFrequencyDominantAllele > 1:
+        msg.append('--minFrequencyDominantAllele should be a value between [0, 1]')
+    if args.minGeneCoverage < 0 or args.minGeneCoverage > 100:
+        msg.append('--minGeneCoverage should be a value between [0, 100]')
+    if args.minGeneIdentity < 0 or args.minGeneIdentity > 100:
+        msg.append('--minGeneIdentity should be a value between [0, 100]')
+    if args.notWriteConsensus and args.doubleRun:
+        msg.append('--notWriteConsensus and --doubleRun cannot be used together.'
+                   ' Maybe you only want to use --doubleRun')
+
+    if len(msg) > 0:
+        argparse.ArgumentParser.error('\n'.join(msg))
+
+    start_time = time.time()
+
+    number_samples_successfully, samples_total_number = run_rematch(args)
+
+    print('\n' + 'END ReMatCh')
+    print('\n' +
+          str(number_samples_successfully) + ' samples out of ' + str(samples_total_number) + ' run successfully')
+    time_taken = utils.run_time(start_time)
+    del time_taken
+
+    if number_samples_successfully == 0:
+        sys.exit('No samples run successfully!')
+
+
+if __name__ == "__main__":
+    main()

README.md

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/utils/README.md

README.md

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/README.md Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,183 @@
+ReMatCh
+=======
+*Reads mapping against target sequences, checking mapping and consensus sequences production*
+
+<https://github.com/B-UMMI/ReMatCh>
+
+Table of Contents
+--
+
+[Combine alignment consensus](#combine-alignment-consensus)
+[Convert Ns to gaps](#convert-ns-to-gaps)
+[gffParser](#gffparser)
+[Restart ReMatCh](#restart-rematch)
+[Strip Alignment](#strip-alignment)
+
+
+## Combine Alignment Consensus
+
+Combine the alignment consensus sequences from ReMatCh first run by reference sequences into single files.
+
+**Dependencies**
+- Python v3
+
+**Usage**
+
+    usage: combine_alignment_consensus.py [-h] [--version]
+                      -w                 /path/to/rematch/working/directory/
+                      [-o /path/to/output/directory/]
+
+    Combine the alignment consensus sequences from ReMatCh first run by reference sequences into single files
+
+    optional arguments:
+                    -h, --help show this help message and exit
+                    --version Version information
+
+    Required options:
+                    -w /path/to/rematch/working/directory/
+                    --workdir /path/to/rematch/working/directory/ Path to the directory where ReMatCh was running (default: None)
+
+    General facultative options:
+                    -o --outdir /path/to/output/directory/  Path to the directory where the combined sequence files will stored (default: .)
+
+
+
+## Convert Ns to Gaps
+
+
+Convert the Ns into gaps in a fasta file.
+
+**Dependencies**
+- Python (2.7.x)
+
+**Usage**
+
+    usage: convert_Ns_to_gaps.py [-h] [--version]
+                    -i /path/to/input/file.fasta
+                    -o                     /path/to/converted/output/file.fasta
+
+    Convert the Ns into gaps
+
+    optional arguments:
+                    -h, --help show this help message and exit
+                    --version Version information
+
+    Required options:
+                    -i --infile /path/to/input/file.fasta Path to the fasta file (default: None)
+                    -o --outfile  /path/to/converted/output/file.fasta                        Converted output fasta file (default:                        converted_Ns_to_gaps.fasta)
+
+
+
+## gffParser
+
+
+Parser for GFF3 files, as the ones obtained by [PROKKA](https://github.com/tseemann/prokka). This files require to have both the features and sequence. It will retrieve the CDS sequences in the GFF file, allowing these to be extended by the number of nucleotides specifiend in `--extraSeq`. A selection of CDS of interest to be parsed can also be obtained by providing `--select` with a txt file of the IDs of interest, one per line. As an alternative, wanted sequences can be obtained from the GFF file from a txt file containing the coontig ID, start and end position (one per line) of the sequences of interest, using the `-fromFile` option. `-extraSeq` can also be obtain through this method.
+
+**Dependencies**
+- Python (2.7.x)
+- [Biopython](http://biopython.org/) (1.68 or similar)
+
+**Usage**
+
+    usage: gffParser.py [-h]
+                    -i INPUT [-x EXTRASEQ] [-k] [-o OUTPUTDIR]
+                   [-s SELECT] [-f FROMFILE] [--version]
+
+   GFF3 parser for feature sequence retrival, containing both sequences and annotations.
+
+ optional arguments:
+                    -h, --help    Show this help message and exit
+                    -i --input INPUT
+                                  GFF3 file to parse, containing both sequences and annotations (like the one obtained from PROKKA).
+                    -x --extraSeq EXTRASEQ
+                                  Extra sequence to retrieve per feature in gff.
+                    -k, --keepTemporaryFiles
+                                  Keep temporary gff(without sequence) and fasta files.
+                    -o --outputDir OUTPUTDIR
+                                  Path to where the output is to be saved.
+                    -s --select SELECT
+                                  txt file with the IDs of interest, one per line
+                    -f --fromFile FROMFILE
+                                  Sequence coordinates to be retrieved. Requires contig ID and coords (contig,strart,end) in a csv file, one per line.
+                    --version     Display version, and exit.
+
+**Output**
+
+*<filename>.fasta*
+Multi-fasta file with the retrieved sequences.
+Headers will contain the feature ID, followed by '=', and the position of that feature in the sequence, starting with the original sequence ID,a '# and' the start and end coordinates separated with '_' (>featureID=contig#start_end).
+If the `--fromFile` option is used, there's no feature ID, so the header will only contain it's position in the original sequence, followed by the start and end coordinates separated with '_' (>contig#start_end).
+
+*<filename>.txt*
+Feature ID of the sequences that failed to be retireved, due to the start position or end position being outside of the sequence where the feature is (due to the `--extraSeq` option).
+
+
+
+## Restart ReMatCh
+
+
+Restart a ReMatCh run abruptly terminated
+
+**Dependencies**
+- Python (2.7.x)
+
+**Usage**
+
+    usage: restart_rematch.py [-h] [--version] -i
+                            /path/to/initial/workdir/directory/
+                            [-w /path/to/workdir/directory/] [-j N]
+                            [--runFailedSamples]
+
+    Restart a ReMatCh run abruptly terminated
+
+    optional arguments:
+                    -h, --help    show this help message and exit
+                    --version     Version information
+
+    Required options:
+                    -i /path/to/initial/workdir/directory/, --initialWorkdir /path/to/initial/workdir/directory/
+                                  Path to the directory where ReMatCh was running (default: None)
+
+  General facultative options:
+                    -w, --workdir /path/to/workdir/directory/
+                                  Path to the directory where ReMatCh will run again (default: .)
+                    -j N, --threads N
+                                  Number of threads to use instead of the ones set in initial ReMatCh run (default: None)
+                    --runFailedSamples
+                                  Will run ReMatCh for those samples missing, as well as for samples that did not run successfully in initial ReMatCh run (default: False)
+
+
+
+## Strip Alignment
+
+
+Strip alignment positions containing gaps,
+missing data and invariable positions.
+
+**Dependencies**
+- Python (2.7.x)
+- [Biopython](http://biopython.org/) (1.68 or similar)
+
+**Usage**
+
+    usage: strip_alignment.py [-h] [--version]
+                    -i                      /path/to/aligned/input/file.fasta -o /path/to/stripped/output/file.fasta [--notGAPs]
+                    [--notMissing] [--notInvariable]
+
+    Strip alignment positions containing gaps, missing data and invariable positions
+
+    optional arguments:
+                    -h, --help    show this help message and exit
+                    --version     Version information
+
+    Required options:
+                    -i, --infile /path/to/aligned/input/file.fasta
+                                  Path to the aligned fasta file (default: None)
+                    -o, --outfile /path/to/stripped/output/file.fasta
+                                  Stripped output fasta file (default: alignment_stripped.fasta)
+
+    General facultative options:
+                    --notGAPs     Not strip positions with GAPs (default: False)
+                    --notMissing  Not strip positions with missing data (default: False)
+                    --notInvariable
+                                  Not strip invariable sites (default: False)

scripts/ReMatCh/utils/combine_alignment_consensus.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/utils/combine_alignment_consensus.py

scripts/ReMatCh/utils/combine_alignment_consensus.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/combine_alignment_consensus.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,120 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+"""
+combine_alignment_consensus.py - Combine the alignment consensus
+sequences from ReMatCh first run by reference sequences into single
+files
+<https://github.com/B-UMMI/ReMatCh/>
+
+Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+
+Last modified: October 15, 2018
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import os
+import argparse
+import time
+import sys
+
+version = '0.2'
+
+
+def concatenate_files(input_files_list, outdir):
+    all_executed_printed = False
+    for x, input_file in enumerate(input_files_list):
+        sample = os.path.basename(input_file).rsplit('.', 2)[0]
+        with open(input_file, 'rtU') as reader:
+            writer = None
+            for line in reader:
+                line = line.rstrip('\r\n')
+                if line.startswith('>'):
+                    file_output = os.path.join(outdir, line[1:] + '.fasta')
+                    if writer is not None:
+                        writer.flush()
+                        writer.close()
+                    if os.path.isfile(file_output):
+                        writer = open(file_output, 'at')
+                    else:
+                        writer = open(file_output, 'wt')
+                    writer.write('>' + sample + '\n')
+                else:
+                    if len(line) > 0:
+                        writer.write(line + '\n')
+            writer.flush()
+            writer.close()
+
+        if (x + 1) % 100 == 0:
+            print('\n' + str(round((float(x + 1) / len(input_files_list)) * 100, 2)) + '% of IDs already processed')
+            all_executed_printed = True
+    if not all_executed_printed:
+        print('\n' + str(round((float(x + 1) / len(input_files_list)) * 100, 2)) + '% of IDs already processed')
+
+
+def combine_alignment_consensus(args):
+    outdir = os.path.abspath(args.outdir)
+    if not os.path.isdir(outdir):
+        os.makedirs(outdir)
+
+    outdir = os.path.join(outdir, 'combine_alignment_consensus_' + time.strftime("%Y%m%d-%H%M%S"), '')
+    os.makedirs(outdir)
+
+    workdir = os.path.abspath(args.workdir)
+
+    alignment_files = []
+    directories = [d for d in os.listdir(workdir) if
+                   not d.startswith('.') and
+                   os.path.isdir(os.path.join(workdir, d, ''))]
+    for sample_dir in directories:
+        sample_dir_path = os.path.join(workdir, sample_dir, '')
+        files = [f for f in os.listdir(sample_dir_path) if
+                 not f.startswith('.') and
+                 os.path.isfile(os.path.join(sample_dir_path, f))]
+        for file_found in files:
+            if file_found.endswith('.alignment.fasta'):
+                file_found_path = os.path.join(sample_dir_path, file_found)
+                alignment_files.append(file_found_path)
+
+    if len(alignment_files) > 0:
+        concatenate_files(alignment_files, outdir)
+    else:
+        sys.exit('No ReMatCh alignment.fasta files were found!')
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='combine_alignment_consensus.py',
+                                     description='Combine the alignment consensus sequences from ReMatCh first run by'
+                                                 ' reference sequences into single'
+                                                 ' files', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
+
+    parser_required = parser.add_argument_group('Required options')
+    parser_required.add_argument('-w', '--workdir', type=str, metavar='/path/to/rematch/working/directory/',
+                                 help='Path to the directory where ReMatCh was running', required=True)
+
+    parser_optional_general = parser.add_argument_group('General facultative options')
+    parser_optional_general.add_argument('-o', '--outdir', type=str, metavar='/path/to/output/directory/',
+                                         help='Path to the directory where the combined sequence files will stored',
+                                         required=False, default='.')
+
+    args = parser.parse_args()
+
+    combine_alignment_consensus(args)
+
+
+if __name__ == "__main__":
+    main()

scripts/ReMatCh/utils/convert_Ns_to_gaps.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/utils/convert_Ns_to_gaps.py

scripts/ReMatCh/utils/convert_Ns_to_gaps.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/convert_Ns_to_gaps.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+"""
+convert_Ns_to_gaps.py - Convert the Ns into gaps
+<https://github.com/B-UMMI/ReMatCh/>
+
+Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+
+Last modified: October 15, 2018
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import os
+import argparse
+
+
+version = '0.2'
+
+
+def conversion(infile, outfile):
+    last_printed = 0
+    counter = 1
+    with open(infile, 'rtU') as reader:
+        with open(outfile, 'wt') as writer:
+            for line in reader:
+                line = line.rstrip('\r\n')
+                if line.startswith('>'):
+                    writer.write(line + '\n')
+                    if counter % 10 == 0:
+                        print('\n' + str(counter) + ' sequences already processed')
+                        last_printed = counter
+                    counter += 1
+                else:
+                    if len(line) > 0:
+                        line = line.replace('N', '-')
+                        writer.write(line + '\n')
+    if last_printed < counter:
+        print('\n' + str(counter - 1) + ' sequences already processed')
+
+
+def convert_n_2_gaps(args):
+    outdir = os.path.dirname(os.path.abspath(args.outfile))
+    if not os.path.isdir(outdir):
+        os.makedirs(outdir)
+
+    outfile = os.path.abspath(args.outfile)
+
+    infile = os.path.abspath(args.infile.name)
+
+    conversion(infile, outfile)
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='convert_Ns_to_gaps.py', description='Convert the Ns into gaps',
+                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
+
+    parser_required = parser.add_argument_group('Required options')
+    parser_required.add_argument('-i', '--infile', type=argparse.FileType('r'), metavar='/path/to/input/file.fasta',
+                                 help='Path to the fasta file', required=True)
+    parser_required.add_argument('-o', '--outfile', type=str, metavar='/path/to/converted/output/file.fasta',
+                                 help='Converted output fasta file', required=True,
+                                 default='converted_Ns_to_gaps.fasta')
+
+    args = parser.parse_args()
+
+    convert_n_2_gaps(args)
+
+
+if __name__ == "__main__":
+    main()

scripts/ReMatCh/utils/gffParser.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/utils/gffParser.py

scripts/ReMatCh/utils/gffParser.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/gffParser.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,225 @@
+#!/usr/bin/env python3
+
+import argparse
+import os
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+import ntpath
+
+version = '1.0'
+
+
+def parse_id(filename):
+    # get wanted feature IDs
+    gff_ids = []
+    with open(filename, 'r') as in_handle:
+        for line in in_handle:
+            line = line.strip()
+            gff_ids.append(line)
+    return gff_ids
+
+
+def retrieve_seq_file(fasta_file, coord_file, extra_seq, filename, output_dir):
+    # Parsing the sequence file, using the provided txt file containing the contig ID and positions to retrieve sequences.
+    handle = open(fasta_file, "rU")
+    records_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
+    handle.close()
+
+    seq_2_get = {}
+    with open(coord_file, 'r') as sequeces2get:
+        for line in sequeces2get:
+            line = line.split(',')
+            coords = (int(line[-2]), int(line[-1]))
+            contig_id = line[0]
+            if contig_id in list(seq_2_get.keys()):
+                seq_2_get[contig_id].append(coords)
+            else:
+                seq_2_get[contig_id] = [coords]
+
+    with open(output_dir + '/' + filename + '.fasta', 'w') as output_handle:
+        fails = 0
+        successes = 0
+        records = []
+        for contig, listCoords in list(seq_2_get.items()):
+            contig_seq = records_dict[contig].seq
+            for coord in listCoords:
+                coord1 = coord[0] - extra_seq
+                coord2 = coord[1] + extra_seq
+                if coord1 < 0 or coord2 > len(contig_seq):
+                    fail_log = open(output_dir + '/' + filename + '_fails.txt', 'a')
+                    fail_log.write(contig + ',' + str(coord[0]) + ',' + str(coord[1]) + '\n')
+                    fail_log.close()
+                    fails += 1
+                else:
+                    geneseq = str(contig_seq[coord1:coord2])
+                    record = SeqRecord(Seq(geneseq), id=str(str(contig) + '#' + str(coord1) + '_' + str(coord2)),
+                                       description='')
+                    records.append(record)
+                    successes += 1
+        SeqIO.write(records, output_handle, "fasta")
+
+    print('Retrived %s features successfully from %s with %s bp as extra'
+          ' sequence.' % (str(successes), filename, str(extra_seq)))
+    if fails > 0:
+        print('%s featrued failed to retrieve. Check %s_fails.txt file.' % (str(fails), filename))
+
+
+def retrieve_seq(fasta_file, gff_features, extra_seq, filename, output_dir):
+    # parsing the sequence file into a SeqIO dictionary. one contig per entry
+    handle = open(fasta_file, "rU")
+    records_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
+    handle.close()
+
+    with open(output_dir + '/' + filename + '.fasta', 'w') as output_handle:
+        fails = 0
+        successes = 0
+        records = []
+        for locus, location in list(gff_features.items()):
+            # print locus
+            contig_seq = records_dict[location[0]].seq
+            coord1 = location[1] - extra_seq
+            coord2 = location[2] + extra_seq
+            if coord1 < 0 or coord2 > len(contig_seq):
+                fail_log = open(output_dir + '/' + filename + '_fails.txt', 'a')
+                fail_log.write(locus + '\n')
+                fail_log.close()
+                fails += 1
+            else:
+                geneseq = str(contig_seq[coord1:coord2])
+                if location[3] == '-':
+                    seq = Seq(geneseq)
+                    geneseq = str(seq.reverse_complement())
+                record = SeqRecord(Seq(geneseq),
+                                   id=str(locus + '-' + str(location[0]) + '#' + str(location[1]) + '_' +
+                                          str(location[2])),
+                    ..('##'):
+                    if '\t' in line:
+                        if select_ids is not None:
+                            items = line.split('\t')
+                            id = items[-1].split(';')[0]
+                            id = id.split('=')[1]
+                            if id in select_ids:
+                                temp_genes.write(line)
+                        else:
+                            temp_genes.write(line)
+                    else:
+                        temp_contigs.write(line)
+
+        gff_files = parse_features(output_dir + '/' + filename + '_features.gff')
+
+        retrieve_seq(output_dir + '/' + filename + '_sequence.fasta', gff_files, extra_seq, filename, output_dir)
+
+    else:
+        with open(gff_file, 'r') as in_handle, \
+                open(output_dir + '/' + filename + '_sequence.fasta', 'a') as temp_contigs:
+            for line in in_handle:
+                if not line.startswith('##'):
+                    if '\t' in line:
+                        pass
+                    else:
+                        temp_contigs.write(line)
+
+        retrieve_seq_file(output_dir + '/' + filename + '_sequence.fasta', coord_file, extra_seq, filename, output_dir)
+
+    # removing temp files
+    if not keep_temporary_files:
+        try:
+            os.remove(output_dir + '/' + filename + '_features.gff')
+        except:
+            pass
+        os.remove(output_dir + '/' + filename + '_sequence.fasta')
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='gffParser.py', description='GFF3 parser for feature sequence retrival.',
+                                     epilog='by C I Mendes (cimendes@medicina.ulisboa.pt)')
+    parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
+
+    parser.add_argument('-i', '--input',
+                        help='GFF3 file to parse, containing both sequences and annotations (like the one obtained from'
+                             ' PROKKA).', type=argparse.FileType('r'), required=True)
+    parser.add_argument('-x', '--extraSeq', help='Extra sequence to retrieve per feature in gff.', default=0, type=int,
+                        required=False)
+    parser.add_argument('-k', '--keepTemporaryFiles', help='Keep temporary gff(without sequence) and fasta files.',
+                        action='store_true')
+    parser.add_argument('-o', '--outputDir', help='Path to where the output is to be saved.', default='.',
+                        required=False)
+
+    parser_optional_selected_regions_exclusive = parser.add_mutually_exclusive_group()
+    parser_optional_selected_regions_exclusive.add_argument('-s', '--select',
+                                                            help='txt file with the IDs of interest, one per line',
+                                                            type=argparse.FileType('r'), required=False)
+    parser_optional_selected_regions_exclusive.add_argument('-f', '--fromFile',
+                                                            help='Sequence coordinates to be retrieved. Requires contig'
+                                                                 ' ID and coords (contig,strart,end) in a csv file. One'
+                                                                 ' per line.', type=argparse.FileType('r'),
+                                                            required=False)
+
+    args = parser.parse_args()
+
+    args.outputDir = os.path.abspath(args.outputDir)
+    if not os.path.isdir(args.outputDir):
+        os.makedirs(args.outputDir)
+
+    gff_parser(os.path.abspath(args.input.name), args.extraSeq, os.path.abspath(args.outputDir),
+               args.keepTemporaryFiles,
+               os.path.abspath(args.select.name) if args.select is not None else None,
+               os.path.abspath(args.fromFile.name) if args.fromFile is not None else None)
+
+
+if __name__ == "__main__":
+    main()

scripts/ReMatCh/utils/restart_rematch.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/utils/restart_rematch.py

scripts/ReMatCh/utils/restart_rematch.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/restart_rematch.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,303 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+"""
+restart_rematch.py - Restarts a ReMatCh run abruptly terminated
+<https://github.com/B-UMMI/ReMatCh/>
+
+Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+
+Last modified: October 15, 2018
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import os
+import argparse
+import subprocess
+import time
+
+
+version = '0.1'
+
+
+def run_rematch(args):
+    print('\n' + '==========> Restarting ReMatCh <==========' + '\n')
+
+    workdir = os.path.abspath(args.workdir)
+    if not os.path.isdir(workdir):
+        os.makedirs(workdir)
+
+    initial_workdir = os.path.abspath(args.initialWorkdir)
+
+    files_required = get_files_required(initial_workdir)
+
+    samples_run = get_samples_run(files_required['sample_report']['file'])
+
+    command, list_ids, taxon, threads, initial_present_directory = get_rematch_command(files_required['run']['file'])
+
+    samples_fastq = {}
+
+    if list_ids is not None:
+        total_samples = get_list_ids_from_file(list_ids)
+    elif taxon:
+        total_samples = get_taxon_run_ids(files_required['IDs_list.seqFromWebTaxon']['file'])
+    else:
+        samples_fastq = search_fastq_files(initial_workdir)
+        total_samples = list(samples_fastq.keys())
+
+    samples_to_run = list(set(total_samples).symmetric_difference(set(sum(list(samples_run.values()), []) if
+                                                                      not args.runFailedSamples else
+                                                                      samples_run['True'] if
+                                                                      'True' in samples_run else [''])))
+
+    print(str(len(samples_to_run)) + ' samples out of ' + str(len(total_samples)) + ' will be analysed by'
+                                                                                    ' ReMatCh' + '\n')
+
+    if list_ids is not None or taxon:
+        samples_to_run_file = write_samples_to_run(samples_to_run, workdir)
+    else:
+        set_samples_from_folders(samples_to_run, samples_fastq, workdir)
+
+    command.extend(['-w', workdir])
+    command.extend(['-j', str(threads) if args.threads is None else str(args.threads)])
+    if list_ids is not None or taxon:
+        command.extend(['-l', samples_to_run_file])
+
+    print('ReMatCh will start in 5 seconds...')
+    time.sleep(5)
+
+    os.chdir(initial_present_directory)
+    subprocess.call(command)
+
+
+def write_samples_to_run(samples_to_run, workdir):
+    samples_to_run_file = os.path.join(workdir, 'restart_rematch.samples_to_run.txt')
+    with open(samples_to_run_file, 'wt') as writer:
+        for sample in samples_to_run:
+            writer.write(sample + '\n')
+    return samples_to_run_file
+
+
+def get_files_required(initial_workdir):
+    files_required = {'sample_report': {'extension': 'tab'},
+                      'run': {'extension': 'log'},
+                      'IDs_list.seqFromWebTaxon': {'extension': 'tab'}}
+    files = sorted([f for f in os.listdir(initial_workdir) if
+                    not f.startswith('.') and
+                    os.path.isfile(os.path.join(initial_workdir, f))])
+    for file_found in files:
+        file_path = os.path.join(initial_workd.._workdir) if
+                   not d.startswith('.') and
+                   os.path.isdir(os.path.join(initial_workdir, d, ''))]
+    for directory_found in directories:
+        directory_path = os.path.join(initial_workdir, directory_found, '')
+
+        fastq_found = []
+        files = [f for f in os.listdir(directory_path) if
+                 not f.startswith('.') and
+                 os.path.isfile(os.path.join(directory_path, f))]
+        for file_found in files:
+            if file_found.endswith(tuple(files_extensions)):
+                fastq_found.append(file_found)
+
+        if len(fastq_found) == 1:
+            list_ids[directory_found] = [os.path.join(directory_path, f) for f in fastq_found]
+        elif len(fastq_found) >= 2:
+            file_pair = []
+
+            # Search pairs
+            for pe_separation in pair_end_files_separation:
+                for fastq in fastq_found:
+                    if pe_separation[0] in fastq or pe_separation[1] in fastq:
+                        file_pair.append(fastq)
+
+                if len(file_pair) == 2:
+                    break
+                else:
+                    file_pair = []
+
+            # Search single
+            if len(file_pair) == 0:
+                for pe_separation in pair_end_files_separation:
+                    for fastq in fastq_found:
+                        if pe_separation[0] not in fastq or pe_separation[1] not in fastq:
+                            file_pair.append(fastq)
+
+                if len(file_pair) >= 1:
+                    file_pair = file_pair[0]
+
+            if len(file_pair) >= 1:
+                list_ids[directory_found] = [os.path.join(directory_path, f) for f in file_pair]
+
+    return list_ids
+
+
+def set_samples_from_folders(samples_to_run, samples_fastq, workdir):
+    for sample in samples_to_run:
+        sample_dir = os.path.join(workdir, sample, '')
+        if not os.path.isdir(sample_dir):
+            os.mkdir(sample_dir)
+        for file_found in samples_fastq[sample]:
+            link_path = os.path.join(sample_dir, os.path.basename(file_found))
+            if os.path.islink(link_path):
+                os.remove(link_path)
+            if not os.path.isfile(link_path):
+                os.symlink(file_found, link_path)
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='restart_rematch.py', description='Restart a ReMatCh run abruptly terminated',
+                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
+
+    parser_required = parser.add_argument_group('Required options')
+    parser_required.add_argument('-i', '--initialWorkdir', type=str, metavar='/path/to/initial/workdir/directory/',
+                                 help='Path to the directory where ReMatCh was running', required=True)
+
+    parser_optional_general = parser.add_argument_group('General facultative options')
+    parser_optional_general.add_argument('-w', '--workdir', type=str, metavar='/path/to/workdir/directory/',
+                                         help='Path to the directory where ReMatCh will run again', required=False,
+                                         default='.')
+    parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N',
+                                         help='Number of threads to use instead of the ones set in initial ReMatCh run',
+                                         required=False)
+    parser_optional_general.add_argument('--runFailedSamples', action='store_true',
+                                         help='Will run ReMatCh for those samples missing, as well as for samples that'
+                                              ' did not run successfully in initial ReMatCh run')
+
+    args = parser.parse_args()
+
+    run_rematch(args)
+
+
+if __name__ == "__main__":
+    main()

scripts/ReMatCh/utils/strip_alignment.py

diff -r 000000000000 -r 8be2feb96994 scripts/ReMatCh/utils/strip_alignment.py

scripts/ReMatCh/utils/strip_alignment.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/strip_alignment.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,183 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+"""
+strip_alignment.py - Strip alignment positions containing gaps,
+missing data and invariable positions
+<https://github.com/B-UMMI/ReMatCh/>
+
+Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+
+Last modified: October 15, 2018
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from Bio import SeqIO
+import os
+import argparse
+import sys
+
+
+version = '0.2'
+
+
+def get_sequences(infile):
+    print('Getting sequences')
+    sequences_seq_io = list(SeqIO.parse(infile, 'fasta'))
+
+    sequence_length = None
+    sequences_dict = {}
+    all_executed_printed = False
+    for x, sequence in enumerate(sequences_seq_io):
+        if sequence_length is None:
+            sequence_length = len(sequence.seq)
+        if sequence_length != len(sequence.seq):
+            sys.exit('Sequences with different length!')
+        sequences_dict[sequence.id] = list(sequence.seq)
+
+        if (x + 1) % 10 == 0:
+            print('\n' + str(round((float(x + 1) / len(sequences_seq_io)) * 100, 2)) + '% of sequences already processed (getting sequences)')
+            if x + 1 == len(sequences_seq_io):
+                all_executed_printed = True
+    if not all_executed_printed:
+        print('\n' + str(round((float(x + 1) / len(sequences_seq_io)) * 100, 2)) + '% of sequences already processed (getting sequences)')
+
+    return sequences_dict, sequence_length
+
+
+def positions_type(sequences_dict, sequence_length, not_gaps, not_missing, not_invariable):
+    print('Determining positions type')
+    positions_2_keep = []
+    invariable = []
+    missing = []
+    gaps = []
+    gaps_missing = 0
+    all_executed_printed = False
+    for i in range(0, sequence_length):
+        data = []
+        for sample in sequences_dict:
+            data.append(sequences_dict[sample][i])
+        possibilities = set(data)
+        if len(possibilities) == 1:
+            invariable.append(i)
+        if len(possibilities.intersection(set(['N']))) > 0:
+            missing.append(i)
+        if len(possibilities.intersection(set(['-']))) > 0:
+            gaps.append(i)
+        if len(possibilities.intersection(set(['N', '-']))) > 0:
+            gaps_missing += 1
+        if len(possibilities) > 1 and len(possibilities.intersection(set(['N', '-']))) == 0:
+            positions_2_keep.append(i)
+
+        if (i + 1) % 10000 == 0:
+            print('\n' + str(round((float(i + 1) / sequence_length) * 100, 2)) + '% of positions already'
+                                                                                 ' processed (determining positions'
+                                                                                 ' type)')
+            if i + 1 == len(sequences_dict):
+                all_executed_printed = True
+        if not all_executed_printed:
+            print('\n' + str(round((float(i + 1) / sequence_length) * 100, 2)) + '% of positions already'
+                                                                                 ' processed (determining positions'
+                                                                                 ' type)')
+
+    print('Positions to keep (no matter): ' + str(len(positions_2_keep)))
+    print..ing data: ' + str(gaps_missing))
+
+    if not_gaps:
+        positions_2_keep.extend(gaps)
+    if not_missing:
+        positions_2_keep.extend(missing)
+    if not_invariable:
+        positions_2_keep.extend(invariable)
+
+    positions_2_keep = sorted(set(positions_2_keep))
+
+    print('Positions to keep (final): ' + str(len(positions_2_keep)))
+
+    return positions_2_keep
+
+
+def chunkstring(string, length):
+    return (string[0 + i:length + i] for i in range(0, len(string), length))
+
+
+def write_fasta(sequences_dict, positions_2_keep, outfile):
+    print('Writing stripped sequences')
+    all_executed_printed = False
+    with open(outfile, 'wt') as writer:
+        for x, sample in enumerate(sequences_dict):
+            writer.write('>' + sample + '\n')
+            fasta_sequence_lines = chunkstring(''.join([sequences_dict[sample][i] for i in positions_2_keep]), 80)
+            for line in fasta_sequence_lines:
+                writer.write(line + '\n')
+
+            if (x + 1) % 100 == 0:
+                print('\n' + str(round((float(x + 1) / len(sequences_dict)) * 100, 2)) + '% of sequences already'
+                                                                                         ' processed (writing stripped'
+                                                                                         ' sequences)')
+                if x + 1 == len(sequences_dict):
+                    all_executed_printed = True
+        if not all_executed_printed:
+            print('\n' + str(round((float(x + 1) / len(sequences_dict)) * 100, 2)) + '% of sequences already'
+                                                                                     ' processed (writing stripped'
+                                                                                     ' sequences)')
+
+
+def strip_alignment(args):
+    outdir = os.path.dirname(os.path.abspath(args.outfile))
+    if not os.path.isdir(outdir):
+        os.makedirs(outdir)
+
+    outfile = os.path.abspath(args.outfile)
+
+    infile = os.path.abspath(args.infile.name)
+
+    sequences_dict, sequence_length = get_sequences(infile)
+    positions_2_keep = positions_type(sequences_dict, sequence_length, args.notGAPs, args.notMissing,
+                                      args.notInvariable)
+    write_fasta(sequences_dict, positions_2_keep, outfile)
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='strip_alignment.py',
+                                     description='Strip alignment positions containing gaps, missing data and'
+                                                 ' invariable positions',
+                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
+
+    parser_required = parser.add_argument_group('Required options')
+    parser_required.add_argument('-i', '--infile', type=argparse.FileType('r'),
+                                 metavar='/path/to/aligned/input/file.fasta', help='Path to the aligned fasta file',
+                                 required=True)
+    parser_required.add_argument('-o', '--outfile', type=str, metavar='/path/to/stripped/output/file.fasta',
+                                 help='Stripped output fasta file', required=True, default='alignment_stripped.fasta')
+
+    parser_optional_general = parser.add_argument_group('General facultative options')
+    parser_optional_general.add_argument('--notGAPs', action='store_true', help='Not strip positions with GAPs')
+    parser_optional_general.add_argument('--notMissing', action='store_true',
+                                         help='Not strip positions with missing data')
+    parser_optional_general.add_argument('--notInvariable', action='store_true', help='Not strip invariable sites')
+
+    args = parser.parse_args()
+
+    strip_alignment(args)
+
+
+if __name__ == "__main__":
+    main()

scripts/__init__.py

diff -r 000000000000 -r 8be2feb96994 scripts/__init__.py

scripts/__init__.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/__init__.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,1 @@
+__version__ = '1.0'

scripts/duk

diff -r 000000000000 -r 8be2feb96994 scripts/duk

scripts/duk

Binary file scripts/duk has changed

scripts/fastq_pair

diff -r 000000000000 -r 8be2feb96994 scripts/fastq_pair

scripts/fastq_pair

Binary file scripts/fastq_pair has changed

scripts/filter_spades_repeats.pl

diff -r 000000000000 -r 8be2feb96994 scripts/filter_spades_repeats.pl

scripts/filter_spades_repeats.pl

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/filter_spades_repeats.pl Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,313 @@
+#!/usr/bin/env perl
+
+use strict;
+use Getopt::Long;
+use Bio::SeqIO;
+use Pod::Usage;
+
+my ($fasta_file, $tab_file, $coverage_co, $length_co, $repeat_co, $out_filtered, $out_repeats, $out_norepeats,$coverage_length_co, $summary_out, $filtered_repeats, $help);
+
+GetOptions(
+ 'c|coverage-cutoff=s'        => \$coverage_co,
+ 'l|length-cutoff=s'        => \$length_co,
+        'e|coverage-length-cutoff=s'   => \$coverage_length_co,
+ 'r|repeat_cutoff=s'        => \$repeat_co,
+ 'i|input=s'        => \$fasta_file,
+ 't|tab=s'        => \$tab_file,
+ 'f|filtered-out=s'        => \$out_filtered,
+ 'o|output-repeats=s'        => \$out_repeats,
+ 'u|output-norepeats=s'        => \$out_norepeats,
+        'n|filtered-repeats=s'         => \$filtered_repeats,
+        's|summary=s'                  => \$summary_out,
+ 'h|help'        => \$help
+);
+
+pod2usage(-verbose => 2) if ($help);
+print "A fasta file is required. Please enter a fasta file using the -i flag.\n" if (!$fasta_file);
+print "A spades tabs file is required. Please enter a tabs file using the -t flag\n" if (!$tab_file);
+pod2usage(1) unless $fasta_file && $tab_file;
+
+if (!$coverage_co)
+{
+   $coverage_co = 0.33;
+}
+if (!$length_co)
+{
+   $length_co = 1000;
+}
+if (!$coverage_length_co)
+{
+   $coverage_length_co = 5000;
+}
+if (!$repeat_co)
+{
+   $repeat_co = 1.75;
+}
+if (!$out_filtered)
+{
+   $out_filtered = "Discarded_sequences.fasta";
+   print "Discarded sequences will be printed out to $out_filtered\n";
+}
+if (!$out_repeats)
+{
+   $out_repeats = "Filtered_sequences_with_repeats.fasta";
+   print "Filtered sequences with repeats will be printed out to $out_repeats\n";
+}
+if (!$out_norepeats)
+{
+   $out_norepeats = "Filtered_sequences_no_repeats.fasta";
+   print "Filtered sequences without repeats will be printed out to $out_norepeats\n";
+}
+if (!$filtered_repeats)
+{
+   $filtered_repeats = "Repeat_sequences.fasta";
+   print "Repeat sequences will be printed out to $filtered_repeats\n";
+}
+
+die ("No tab file specified") unless ($tab_file);
+die ("No fasta file specified") unless ($fasta_file);
+
+##Read tab file and discard rows with comments
+open TAB, '<', $tab_file or die "Could not open tab file: $?";
+open SEQIN, '<', $fasta_file or die "Could not open tab file: $?";
+open SEQOUT_REP, '>', $out_repeats or die "Could not open file for writing: $?";
+open SEQOUT_NOREP, '>', $out_norepeats or die "Could not open file for writing: $?";
+open SEQOUT_FILT, '>', $out_filtered if ($out_filtered);
+open SEQOUT_FILT_REP, '>', $filtered_repeats or die "Could not open file for writing: $?";
+open SUMMARY, '>', $summary_out if ($summary_out);
+
+
+my $avg_coverage = 0;
+my $num_contigs = 0;
+my $cutoff_coverage;
+my $cutoff_repeats;
+my @stats;
+
+
+while (<TAB>)
+{
+ chomp;
+ push @stats, $_ unless (/^#/);
+}
+
+#Calculate average coverage.
+foreach my $stat(@stats)
+{
+ my ($length, $coverage);
+ (undef,$length, $coverage) = split(/\t+/, $stat);
+        die "length or coverage not defined at $stat\n" unless ($length && ($coverage ne '' && $coverage >= 0));
+ if ($length >= $coverage_length_co)
+ {
+ $avg_coverage = $avg_coverage + $coverage;
+ $num_contigs++;
+ }
+}
+
+$avg_coverage = $avg_coverage / $num_contigs;
+$cutoff_coverage = $avg_coverage * $coverage_co;
+$cutoff_repeats = $avg_coverage * $repeat_co;
+
+print SUMMARY "Filter SPAdes repeats Results Summary\n======================================\n\n" if ($summary_out);
+print SUMMARY "Paramaters used:\nLength cutoff for calcularing average cutoff: $coverage_length_co\nCoverage cutoff ratio: $coverage_co\nRepeat cutoff ratio: $repeat_co\nLength cutoff: $length_co\n\n" if ($summary_out);
+
+print SUMMARY "Calculations:\nAverage coverage: $avg_coverage\nCoverage cutoff: $cutoff_coverage\nRepeat cutoff: $cutoff_repeats\n\nFile headers:\n" if ($summary_out);
.." copies)";
+ print SEQOUT_REP $header,"\n";
+                                $filtered_rep = $filtered_rep.$header."\n";
+                                print SEQOUT_FILT_REP $header, "\n";
+                                $repeats = $repeats.$header."\n";
+ $repeated = 1;
+ }
+ else
+ {
+ print SEQOUT_REP $header, "\n";
+                                $filtered_rep = $filtered_rep.$header."\n";
+ print SEQOUT_NOREP $header, "\n";
+                                $filtered_norep = $filtered_norep.$header."\n";
+ $repeated = 0;
+ }
+ }
+ elsif ($out_filtered)
+ {
+ $valid = 0;
+ print SEQOUT_FILT $header,"\n";
+                        $discarded = $discarded.$header."\n";
+ }
+ }
+ else
+ {
+ if ($valid)
+ {
+ print SEQOUT_REP $line;
+ if (!$repeated)
+ {
+ print SEQOUT_NOREP $line;
+ }
+                        else
+                        {
+                              print SEQOUT_FILT_REP $line;
+                        }
+ }
+ elsif ($out_filtered)
+ {
+ print SEQOUT_FILT $line;
+ }
+ }
+
+}
+
+close TAB;
+close SEQIN;
+close SEQOUT_REP;
+close SEQOUT_NOREP;
+close SEQOUT_FILT;
+close SEQOUT_FILT_REP;
+
+
+#Get summary info:
+if ($summary_out)
+{
+   print SUMMARY "Filtered sequences (with repeats):\n$filtered_rep\n";
+   print SUMMARY "Filtered sequences (no repeats):\n$filtered_norep\n";
+   print SUMMARY "Repeat sequences:\n$repeats\n";
+   if ($out_filtered)
+   {
+      print SUMMARY "Discarded sequences:\n$discarded\n";
+   }
+
+   close SUMMARY;
+}
+
+die "More rows in stats file than sequences in the fasta file\n" if (scalar(@stats) > 0);
+exit 0;
+
+
+__END__
+
+
+
+=head1 NAME
+
+ filter_spades_repeats.pl - Filters contigs or scaffolds based on contig length and detects contigs/scaffolds with very high coverage.
+
+
+
+=head1 USAGE
+
+ filter_spades_output.pl -i <contigs/scaffolds input>
+                                -t <stats input>
+                                -o <output fasta with repeats>
+                                -u <output fasta without repeats>
+
+                                Optional:
+                                -c <coverage cutoff ratio> (default 0.33)
+ -l <length cutoff> (default: 1000)
+                                -e <length cutoff for average coverage calculation> (default: 5000)
+ -r <repeat cutoff ratio> (default (1.75)
+                                -n <filtered repeated sequences>
+                                -f <discarded sequences>
+                                -s <output summary file>
+
+                                For more information:
+                                -h
+
+
+=head1 INPUT
+
+=over 8
+
+=item B<-i>B<--input>
+
+Contigs/Scaffolds fasta file.
+
+=item B<-t>B<--tab>
+
+The tabular output file from SPAdes. This file should have the following format:
+
+      #name length   coverage
+
+      NODE_1   31438 24.5116
+
+      NODE_2   31354 2316.96
+
+      NODE_3   26948 82.3294
+
+=item B<-o>B<--output-repeats>
+
+Output fasta file including the contigs marked as repeated.
+
+=item B<-u>B<--output-norepeats>
+
+Output fasta file excluding the contigs marked as repeated.
+
+=item B<-c>B<--coverage-cutoff>
+
+Mininum coverage ratio.
+
+ coverage_theshold = average_coverage * minimum_coverage_ratio.
+
+Any contigs/scaffolds with coverage below the coverage_theshold will be eliminated.
+
+=item B<-l>B<--length-cutoff>
+
+Mininum length. Contigs below this length will be eliminated.
+
+=item B<-e>B<--coverage-length-cutoff>
+
+Minimum length to use for average coverage calculations.
+
+=item B<-r>B<--repeat-cutoff>
+
+Minimum repeats ratio.
+
+ repeat_threshold = average_coverage * repeat_ratio.
+
+Any contigs with coverage below this threshold will be considered to be repeated
+
+
+=item B<-f>B<--filtered-out>
+
+If specified, filtered out sequences will be written to this file.
+
+=item B<-s>B<--summary>
+
+A summary of results
+
+=back
+=cut

scripts/modules/run_rematch.py

diff -r 000000000000 -r 8be2feb96994 scripts/modules/run_rematch.py

scripts/modules/run_rematch.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/modules/run_rematch.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,120 @@
+import functools
+import os
+import sys
+import multiprocessing
+
+try:
+    import modules.utils as utils
+except ImportError:
+    from pathotyping.modules import utils as utils
+
+
+# {'noMatter': '/home/ubuntu/NGStools/patho_typing/mpmachado_stuff.out_test/rematch/sample.noMatter.fasta', 'correct': '/home/ubuntu/NGStools/patho_typing/mpmachado_stuff.out_test/rematch/sample.correct.fasta', 'alignment': '/home/ubuntu/NGStools/patho_typing/mpmachado_stuff.out_test/rematch/sample.alignment.fasta'}
+
+
+def remove_alignment(alignment_file):
+    directory = os.path.dirname(alignment_file)
+    files = [f for f in os.listdir(directory) if not f.startswith('.') and os.path.isfile(os.path.join(directory, f))]
+    for file_found in files:
+        if file_found.startswith(os.path.splitext(os.path.basename(alignment_file))[0]):
+            file_found = os.path.join(directory, file_found)
+            os.remove(file_found)
+
+
+def remove_reference_stuff(outdir, reference_file):
+    files = [f for f in os.listdir(outdir) if not f.startswith('.') and os.path.isfile(os.path.join(outdir, f))]
+    for file_found in files:
+        if file_found.startswith(os.path.splitext(os.path.basename(reference_file))[0]):
+            file_found = os.path.join(outdir, file_found)
+            os.remove(file_found)
+
+
+def clean_rematch_folder(consensus_files, bam_file, reference_file, outdir, doNotRemoveConsensus, debug_mode_true):
+    if not debug_mode_true:
+        if not doNotRemoveConsensus:
+            for consensus_type, file_path in list(consensus_files.items()):
+                if os.path.isfile(file_path):
+                    os.remove(file_path)
+        if bam_file is not None:
+            remove_alignment(bam_file)
+        remove_reference_stuff(outdir, reference_file)
+
+
+def sequence_data(sample, reference_file, bam_file, outdir, threads, length_extra_seq, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele, debug_mode_true, rematch):
+    sequence_data_outdir = os.path.join(outdir, 'sequence_data', '')
+    utils.removeDirectory(sequence_data_outdir)
+    os.mkdir(sequence_data_outdir)
+
+    sequences, headers = utils.get_sequence_information(reference_file, length_extra_seq)
+
+    pool = multiprocessing.Pool(processes=threads)
+    for sequence_counter in sequences:
+        sequence_dir = os.path.join(sequence_data_outdir, str(sequence_counter), '')
+        utils.removeDirectory(sequence_dir)
+        os.makedirs(sequence_dir)
+        pool.apply_async(rematch.analyse_sequence_data, args=(bam_file, sequences[sequence_counter], sequence_dir, sequence_counter, reference_file, length_extra_seq, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele,))
+    pool.close()
+    pool.join()
+
+    run_successfully, sample_data, consensus_files, consensus_sequences = rematch.gather_data_together(sample, sequence_data_outdir, sequences, outdir.rsplit('/', 2)[0], debug_mode_true, length_extra_seq, False)
+
+    return run_successfully, sample_data, consensus_files, consensus_sequences
+
+
+def determine_general_statistics(sample_data, minimum_gene_coverage, minimum_gene_identity):
+    print('Writing report file')
+    number_absent_genes = 0
+    number_genes_multiple_alleles = 0
+    mean_sample_coverage = 0
+
+    with open('output_dir/rematch/rematchModule_report.txt', 'wt') as writer:
+        writer.write('\t'.join(['#gene', 'percentage_gene_coverage', 'gene_mean_read_coverage', 'percentage_gene_low_coverage', 'number_positions_multiple_alleles', 'percentage_gene_identity']) + '\n')
+        for i in range(1, len(sample_data) + 1):
+            writer.write('\t'.join([sample_data[i]['header'], str(round(sample_data[i]['gene_coverage'], 2)), str(round(sample_data[i]['gene_mean_read_coverage'], 2)), str(round(sample_data[i]['gene_low_coverage'], 2)), str(sample_data[i]['gene_number_positions_multiple_alleles']), str(round(sample_data[i]['gene_identity'], 2))]) + '\n')
+
+            if sample_data[i]['gene_coverage'] < minimum_gene_coverage or sample_data[i]['gene_identity'] < minimum_gene_identity:
+                number_absent_genes += 1
+            else:
+                mean_sample_coverage += sample_data[i]['gene_mean_read_coverage']
+                if sample_data[i]['gene_number_positions_multiple_alleles'] > 0:
+                    number_genes_multiple_alleles += 1
+
+        if len(sample_data) - number_absent_genes > 0:
+            mean_sample_coverage = float(mean_sample_coverage) / float(len(sample_data) - number_absent_genes)
+        else:
+            mean_sample_coverage = 0
+
+        writer.write('\n'.join(['#general', '>number_absent_genes', str(number_absent_genes), '>number_genes_multiple_alleles', str(number_genes_multiple_alleles), '>mean_sample_coverage', str(round(mean_sample_coverage, 2))]) + '\n')
+
+        print('\n'.join([str('number_absent_genes: ' + str(number_absent_genes)),
+                     str('number_genes_multiple_alleles: ' + str(number_genes_multiple_alleles)),
+                     str('mean_sample_coverage: ' + str(round(mean_sample_coverage, 2)))]) + '\n')
+
+    return number_absent_genes, number_genes_multiple_alleles, mean_sample_coverage
+
+module_timer = functools.partial(utils.timer, name='Module ReMatCh')
+
+
+@module_timer
+def run_rematch(rematch, outdir, reference_file, bam_file, threads, length_extra_seq, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele, minimum_gene_coverage, minimum_gene_identity, debug_mode_true, doNotRemoveConsensus):
+    module_dir = os.path.join(outdir, 'rematch', '')
+    utils.removeDirectory(module_dir)
+    os.makedirs(module_dir)
+
+    sys.path.append(os.path.join(os.path.dirname(rematch), 'modules'))
+    import rematch_module as rematch
+
+    print('Analysing alignment data')
+    run_successfully, sample_data, consensus_files, consensus_sequences = sequence_data('sample', reference_file, bam_file, module_dir, threads, length_extra_seq, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele, debug_mode_true, rematch)
+
+    if run_successfully:
+        number_absent_genes, number_genes_multiple_alleles, mean_sample_coverage = \
+            determine_general_statistics(sample_data=sample_data, minimum_gene_coverage=minimum_gene_coverage,
+                                         minimum_gene_identity=minimum_gene_identity)
+
+    if not debug_mode_true:
+        utils.removeDirectory(module_dir)
+
+    clean_rematch_folder(consensus_files, bam_file, reference_file, outdir, doNotRemoveConsensus, debug_mode_true)
+
+    return run_successfully, {'number_absent_genes': number_absent_genes if 'number_absent_genes' in locals() else None, 'number_genes_multiple_alleles': number_genes_multiple_alleles if 'number_genes_multiple_alleles' in locals() else None, 'mean_sample_coverage': round(mean_sample_coverage, 2) if 'mean_sample_coverage' in locals() else None}, sample_data if 'sample_data' in locals() else None

scripts/modules/seq_conf/escherichia_coli/typing.config

diff -r 000000000000 -r 8be2feb96994 scripts/modules/seq_conf/escherichia_coli/typing.config

scripts/modules/seq_conf/escherichia_coli/typing.config

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/modules/seq_conf/escherichia_coli/typing.config Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,20 @@
+#reference_file (fasta file full path)
+escherichia_coli.fasta
+#length_extra_seq (int)
+0
+#maximum_number_absent_genes (int)
+1
+#maximum_number_genes_multiple_alleles (int)
+1
+#minimum_read_coverage (x, int)
+25
+#minimum_depth_presence (x, int)
+5
+#minimum_depth_call (x, int)
+10
+#minimum_depth_frequency_dominant_allele (0-1, double)
+0.60
+#minimum_gene_coverage (0-100, int)
+60
+#minimum_gene_identity (0-100, int)
+70

scripts/modules/seq_conf/escherichia_coli/typing.fasta

diff -r 000000000000 -r 8be2feb96994 scripts/modules/seq_conf/escherichia_coli/typing.fasta

scripts/modules/seq_conf/escherichia_coli/typing.fasta

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/modules/seq_conf/escherichia_coli/typing.fasta Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,98756 @@
+>tia_1_U20318
+ATGATTGAAATGAAAAAGGTTATTGCGGTTTCAGCGCTTGCAATGGCAGGTATGTTTTCGGCCCAGGCTCTGGCTGATGA
+GAGCAAAACAGGCTTTTATGTGACCGGTAAAGCCGGTGCTTCAGTTGTGATGCAGACTGACCAGCGCTTCCGTCAGGACT
+TTGGGGATGATGTTTATAAGTATAAGGGCGGTGATAAAAACGATACTGTATTTGGTGCCGGCCTTGCAGTGGGCTATGAT
+TTTTATCAACATTACAATGTTCCAGTACGCACGGAAGTGGAATTCTATGGCCGTGGAGCTGCAGACTCCCGTTATACACT
+GGATACATGGCGTTCTCCGATGGGGGATGGTGGTCGGGAAGACACACAAAATAGGCTCAGTGTGAATACCCTGATGGTGA
+ACACGTATTATGATTTCAGAAACAGCAGTGCATTTACTCCATGGGTATCTGTTGGCCTGGGTTATGCACGGGTACATCAT
+AAGGCGACATATATTGATACCTCCTGGAATGAATCTGGCGAGATAAGTGATATTTCTGCGTTACATTACTCGGGATATGA
+TAACAACTTCGCATGGAGCATTGGGGCCGGTGTTCGCTATGACGTAACCCCGGATATCGCTCTTGACCTCAGCTATCGCT
+ATCTGGATGCTGGTAAATCCTCCCTGTCTTACAAGGATACAGAAGGGGATAAATATAAATCAGAGGCTGACGTTAAAAGT
+CATGACATTATGCTTGGGGTAACTTATCATTTCTGA
+>sth-sta3_1_FN822745
+ATGAAGAAATCAATATTATTTATTTTTCTTTCTGTATTGTCTTTTTCACCTTTCGCTCAGGATGCTAAAC
+CAGTAGAGTCTTCAAAAGAAAAAATCACACTAGAATCAAAAAAATGTAACATTGCAAAAAAAAGTAATAA
+AAGTGGTCCTGAAAGCATGAATAGTAGCAATTACTGCTGTGAATTGTGTTGTAATCCTGCTTGTACCGGG
+TGCTATTAA
+>astA_1_AF161000
+ATGCCATCAACACAGTATATCCGGAGACCCACATCCAGTTATGCATCGTGCATATGGTGCGCAACAGTCTGC
+GCTTCGTGTCATGGAAGGACTACAAAGCCGTCACTCGCGACCTGA
+>astA_2_AF161001
+ATGCCATCAACACAGTATATCCGGAGACCCACATCCAGTTATGCATCGTGCATATGGTGCGCAACAGCGTGC
+GCTTCGTGTCATGGAAGGACTACAAAGCCGTCACTCGCGACCTGA
+>astA_3_AB042005
+ATGCCATCAACACAGTATATCCGGAGGCCCGCATCCAGTTATGCATCGTGCATATGGTGCGCAACAGCCTGC
+GCTTCGTGTCATGGAAGGACTACAAAGCCGTCACTCGCGACCTGA
+>astA_4_AB042002
+ATGCCATCAACACAGTATATCCGAAGGCCCGCATCCAGTTATGCATCGTGCATATGGTGCGCAACAGCCTGC
+GCTTCGTGTCATGGAAGGACTACAAAGCCGTCACTCGCGACCTGA
+>astA_5_AF160998
+ATGCCATCAACACAGTATATCCGGAGGCCAGCATCCAGTTATGCATCGTGCATATGGTGCGCAACAGCCTGC
+GCTTCGTGTCATGGAAGGACTACAAAGCCGTCACTCGCGACCTGA
+>astA_6_AY545598
+ATGCCATCAACACAGTATATCCGAAGGCCCGCATCCAGTTATGCATCGTGCATATGGTGCGCAACAGCCTGC
+GCTTCGTGTCATGGAAGGACTACAAGGCCGTCACTCGCGACCTGA
+>astA_7_AF411067
+ATGCCATCAACGCAGTATATCCGAAGGCCCGCATCCAGTTATGCATCGTGCATATGGTGCGCAACAGCCTGC
+GCTTCGTGTCATGGAAGGACTACAAAGCCGTCACTCGCGACCTGA
+>astA_8_HM099897
+ATGCCATCAACACAGTATATCCGGAGGCCCGCATCCAGTTATGCATCGTGCATATGGTGCGCAACAGCATGC
+GCTTCGTGTCATGGAAGGAATACAAAGCCGTCACTCGCGACCTGA
+>astA_9_AF160995
+ATGCCATCAACACAGTATATCCGAAGGCCCGCATCCAGTTATGCATCGTGCATATGGTGCGCAACAGCGTGC
+GCTTCGTGTCATGGAAGGACTACAAAGCCGTCACTCGCGACCTGA
+>astA_10_L11241
+ATGCCATCAACACAGTATATCCGAAGGCCCGCATCCAGTTATGCATCGTGCATATGGTGCACAACAGCCTGC
+GCTTCGTGTCATGGAAGGACTACAAAGCCGTCACTCGCGACCTGA
+>astA_11_HM099896
+ATGCCATCAACACAGTATATCCGGAGGCCAGCATCCAGTTATGCATCGTGCATATGGTGCGCAACAGCATGC
+GCTTCGTGTCATGGAAGGAATACAAAGCCGTCACTCGCGACCTGA
+>astA_12_KJ149556
+ATGCCATCAACACAGTATATCCGAAGGCCCGCATCCAGTTATGCATAGTGCATATGGTGCGCAACAGTCTGC
+GCTTCGTGTCATGGAAGGACTACAAAGCCGTCACTCGCGACCTGA
+>bfpA_1_AB247925
+ATGGTTTCTAAAATCATGAATAAGAAATACGAAAAAGGTCTGTCTTTGATTGAATCTGCAATGGTGCTTGCG
+CTTGCTGCCACCGTTACCGCAGGTGTGATGTTTTACTACCAGTCTGCGTCTGATTCCAATAAGTCGCAGAAT
+GCTATTTCAGAAGTAATGAGCGCAACGTCTGCAATTAATGGTCTGTATATTGGGCAGACCAGTTATAGTGGA
+TTGGACTCAACGATTTTACTTAACACATCTGCAATTCCGGATAATTACAAAGATACAACAAACAGAAAAATA
+ACCAACCCATTTGGGGGGGAATTAAATGTAGGTCCAGCAAACAATAACACCGCATTTGGTTACTATCTGACG
+CTTACCGGGCTGGATAAAGCGGCATGTGTTAGTCTTGCAACCTTGAACTTAGGTACTTCAGCGAAAGGCTAC
+GGTGTTAATATCTCTAGCGAAAATAACACTACATCATTTGGTAATAGCGCTGATCAGGCTGCTAAATCGACT
+GCTATTACTCCTGCTGAAGCGGCAACTGCATGTAAAAAACCTGATTCAACCAATAAAGTTACATATTTTATG
+AAGTAA
+>bfpA_2_AM114103
+ATGGTTTCTAAAATCATGAATAAGAAATACGAAAAAGGTCTGTCTTTGATTGAATCTGCAATGGTGCTTGCG
+CTTGCTGCCACCGTTACCGCAGGTGTGATGTTTTACTACCAGTCTGCGTCTGATTCCAATAAGTCGCAGAAT
+GCTATTTCAGAAGTAATGAGCGCAACGTCTGCAATTAATGGTCTGTATATTGGGCAGACCAGTTATAGTGGA
+TTGGACTCAACGATTTTACTTAACACATCTGCAATTCCGGATAATTACAAAGATACAACAAACAAAAAAATA
+ACCAACCCATTTGGGGGGGAATTAAATGTAGGTCCAGCAAACAATAACACCGCATTTGGTTACTATCTGACG
+CTTACCGGGCTGGATAAAGCGGCATGTGTTAGCCTTGCAACCTTGAACTTAGGTACTTCAGCGAAAGGCTAC
+GGTGTTAATATCTCTGGCGAAAATAACATTACATCATTTGGTAATGGCGCTG..GGTAGCTATGGCAGTGGTGTCTTTTGGTGTAAATGCTGCTCCAACTATTCCACAGGGGCAGGGTAAAGTAACTTTTAACGGAACTGTTGTTGATGCTCCATGCAGCATTTCTCAGAAATCAGCTGATCAGTCTATTGATTTTGGACAGCTTTCAAAAAGCTTCCTTGAGGCAGGAGGTACATCCAAGCCAATGGATTTAGATATTGAGTTAGTAAATTGCGATATTACAGCTTTTAAACAAGGTCAAGCAGCTAAAAACGGTAAGGTTCAATTATCTTTTACTGGGCCACAAGTAACGGGGCAGGCTGAAGAATTAGCAACTAACGGCGGTACGGGCACAGCTATTGTAGTTCAGGCTGCAGGCAAAAACGTTTCTTTCGATGGGACTGCAGGTGACGCTTATCCCCTGAAAGATGGTGATAATGTTCTTCATTATACAGCTCTTGTGAAAAAAGCGAATGGCGGTACTGTTTCTGAAGGTGCTTTTTCTGCAGTTGCAACCTTTAATTTAAGTTACCAGTAA
+>papA_F13_30_JONC01000026
+ATGATTAAGTCGGTTATTGCCGGTGCGGTAGCTATGGCAGTGGTGTCTTTTGGTGTAAATGCTGCTCCAACTATTCCACAGGGGCAGGGTAAAGTAACTTTTAACGGAACTGTTGTTGATGCTCCATGCAGCATTTCTCAGAAATCAGCTGATCAGTCTATTGATTTTGGACAGCTTTCAAAAAGCTTCCTTGAGGCAGGAGGTGTATCCAAACCAATGGACTTAGATATTGAATTGGTTAATTGTGATATTACTGCCTTTAAAGGTGGTAATGGCGCCCAAAAAGGGACTGTTAAGCTGGCTTTTACTGGCCCGATAGTTAATGGACATTCTGATGAGCTAGATACAAATGGTGGTACGGGCACAGCTATCGTAGTTCAGGGGGCAGGTAAAAACGTTGTCTTCGATGGCTCCGAAGGTGATGCTAATACCCTGAAAGATGGTGAAAACGTGCTGCATTATACTGCTGTTGTTAAGAAGTCGTCAGCCGTTGGTGCCGCTGTTACTGAAGGTGCCTTCTCAGCAGTTGCGAATTTCAACCTGACTTATCAGTAA
+>papA_F7-1_31_M68061
+ATGATTAAGTCGGTTATTGCCGGTGCGGTAGCTATGGCAGTGGTGTCTTTTGGTGCAAATGCAGCTGCATCTATCCCTCAAGGACAAGGTGAAGTAAGTTTTAAAGGGACTGTTGTTGACGCTCCGTGTGGTATTGAAACTCAGTCTGCAAAACAGGAAATTGATTTTGGTCAGATCTCTAAATCCTTCCTGCAAGAGGGGGGAGAGACTCAACCGAAAGATTTGAATATTAAGCTTGTGAATTGTGACATTACTAATTTCAAACAGCTTCAAGGCGGGGCAGCTAAAAAAGGTACAGTGTCATTGACATTTTCAGGTGTGCCTGCAGAAAATGCAGATGACATGCTGCAAACAGTTGGAGATACTAATACTGCGATTGTTGTTACTGATTCGAGTGGAAAACGGGTGAAATTTGATGGAGCCACTGAGACCGGGGCTTCAAATCTGATTAATGGCGATAATACAATTCATTTTACTGCATTTGTTAAGAAAGATAATAGTGGCAAGAATGTAGCTGAAGGTGCCTTCTCAGCAGTTGCGAATTTCAACCTGACTTATCAGTAA
+>papA_F7-1_32_X02921
+ATGATTAAGTCGGTTATTGCCGGTGCGGTAGCTATGGCAGTGGTGTCTTTTGGTGCAAATGCAGCTGCATCTATCCCTCAAGGACAAGGTGAAGTAAGTTTTAAAGGGACTGTTGTTGACGCTCCGTGTGGTATTGAAACTCAGTCTGCAAAACAGGAAATTGATTTTGGTCAGATCTCTAAATCCTTCCTGCAAGAGGGGGGAGAGACTCAACCGAAAGATTTGAATATTAAGCTTGTGAATTGTGACATTACTAATTTGAAACAGCTTCAAGGCGGGGCAGCTAAAAAAGGTACAGTGTCATTGACATTTTCAGGTGTGCCTGCAGAAAATGCAGATGACATGCTGCAAACAGTTGGAGATACTAATACTGCGATTGTTGTTACTGATTCGAGTGGAAAACGGGTGAAATTTGATGGAGCCACTGAGACCGGGGCTTCAAATCTGATTAATGGCGATAATACAATTCATTTTACTGCATTTGTTAAGAAAGATAATAGTGGCAAGAATGTAGCTGAAGGTGCCTTCTCAGCAGTTGCGAATTTCAACCTGACTTATCAGTAA
+>papA_F13_33_X61239
+ATGATTAAGTCGGTTATTGCCGGTGCGGTAGCTATGGCAGTGGTGTCTTTTGGTGTAAATAATGCTGCTCCAACTATTCCACAGGGGCAGGGTAAAGTAACTTTTAACGGAACTGTTGTTGATGCTCCATGCAGCATTTCTCAGAAATCAGCTGATCAGTCTATTGATTTTGGACAGCTTTCAAAAAGCTTCCTTGAGGCAGGAGGTGTATCCAAACCAATGGACTTAGATATTGAATTGGTTAATTGTGATATTACTGCCTTTAAAGGTGGTAATGGCGCCAAAAAAGGGACTGTTAAGCTGGCTTTTACTGGCCCGATAGTTAATGGACATTCTGATGAGCTAGATACAAATGGTGGTACGGGCACAGCTATCGTAGTTCAGGGGGCAGGTAAAAACGTTGTCTTCGATGGCTCCGAAGGTGATGCTAATACCCTGAAAGATGGTGAAAACGTGCTGCATTATACTGCTGTTGTTAAGAAGTCGTCAGCCGTTGGTGCCGCTGTTACTGAAGGTGCCTTCTCAGCAGTTGCGAATTTCAACCTGACTTATCAGTAA
+>papA_F7-2_34_ECOFIMAA
+ATGATTAAGTCGGTTATTGCCGGTGCGGTAGCTATGGCAGTGGTGTCTTTTGGTGCATATGCTGCTCCAACTATTCCTCAGGGGCAGGGTAAAGTAACTTTTAACGGAACTGTAGTAGATGCACCATGTGGTATTGATGCTCAGTCTGCTGATCAATCTATTGATTTTGGACAAGTATCAAAATTATTTCTGGAGAATGATGGGGAAAGTCAACCCAAATCTTTTGATATTAAACTTATAAATTGTGATATTACAAACTTTAAAAAAGCTGCTGGCGGTGGTGGGGCGAAGACTGGCACAGTATCTCTGACTTTTTCGGGTGTCCCAAGTGGTCCGCAGAGTGACATGTTACAGACCGTCGGTGCAACAAATACAGCTATTGTTGTCACCGATCCACATGGAAAACGCGTAAAATTTGATGGTGCGACAGCAACAGGTGTTTCCTATTTAGTTGATGGTGATAACACAATTCATTTTACTGCTGCCGTCAGAAAAGATGGTAGTGGCAACCCTGTAACAGAAGGTGCTTTCTCAGCAGTTGCGAATTTCAACCTGACTTATCAGTAA
+>papA_prsA_F12_1_X62157
+GGTGCAAATGCAGCTCCACAGGGGCAGGGAAAAGTAACTTTTAACGGAACTGTAGTAGATGCACCATGTGGTATTGATGCTCAGTCTGCTGATCAATCTATTGAGTTTGGTCAGGTTTCTAAAGTTTTACTGAATAATGGTGGATCCTCAACGCCCAAGAATTTTGATATAAAACTTACCGATTGTGATGTTACTAACTATAAGAAGGCTGGTAAAGCGGGGACTGTATCTCTGACATTCTCAGGGGTTCAAGCTGGTACCGATATGTTGCAAACAGTTGGTACGACTGGTACAGCAATTCTAGTTAAAGATCCTCATGGCAAAGCAGTAAAATTTGATGGAGCAACAGCGACAGGTGTGTCAAGTCTTGTCGATGGGGATAATACAATCCATTTTACTGCTCTGGTTAAGAAAGACACAAGTGGCAATGATGTAGCTGAAGGTGCCTTCTCAGCAGTTGCGAATTTCAACCTGATTTATCAGTAA
\ No newline at end of file

scripts/modules/typing.py

diff -r 000000000000 -r 8be2feb96994 scripts/modules/typing.py

scripts/modules/typing.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/modules/typing.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,84 @@
+import os.path
+import functools
+
+try:
+    import modules.utils as utils
+except ImportError:
+    from pathotyping.modules import utils as utils
+
+
+# {1: {'gene_identity': 0, 'gene_mean_read_coverage': 0.0, 'gene_number_positions_multiple_alleles': 0, 'header': 'fyuA', 'gene_coverage': 0.0, 'gene_low_coverage': 100.0}}
+
+
+def simplify_data_by_gene(data_by_gene):
+    cleaned_data_by_gene = {}
+    for counter, data in list(data_by_gene.items()):
+        cleaned_data_by_gene[data['header'].lower()] = {'gene_identity': data['gene_identity'],
+                                                        'gene_coverage': data['gene_coverage'],
+                                                        'gene_depth': data['gene_mean_read_coverage']}
+    return cleaned_data_by_gene
+
+
+def possible_types(data_by_gene, typing_rules_file, min_gene_coverage, min_gene_identity, min_gene_depth):
+    data_by_gene = simplify_data_by_gene(data_by_gene)
+
+    possible_pathotypes = []
+    genes_present = []
+    with open(typing_rules_file, 'rtU') as reader:
+        genes = []
+        for line in reader:
+            line = line.splitlines()[0]
+            if len(line) > 0:
+                line = line.split('\t')
+                if not line[0].startswith('##'):
+                    if line[0].startswith('#'):
+                        genes = line[1:]
+                    else:
+                        profile = line[1:]
+                        congruence = []
+                        for x, gene_requirement in enumerate(profile):
+                            if data_by_gene[genes[x].lower()]['gene_coverage'] >= min_gene_coverage and \
+                                    data_by_gene[genes[x].lower()]['gene_identity'] >= min_gene_identity and \
+                                    data_by_gene[genes[x].lower()]['gene_depth'] >= min_gene_depth:
+                                gene_present = True
+                                genes_present.append(genes[x])
+                            else:
+                                gene_present = False
+
+                            gene_requirement = \
+                                True if gene_requirement == '1' else False if gene_requirement == '0' else None
+                            if gene_requirement is not None:
+                                if gene_present == gene_requirement:
+                                    congruence.append(True)
+                                else:
+                                    congruence.append(False)
+                            else:
+                                congruence.append(True)
+                        if all(congruence):
+                            possible_pathotypes.append(line[0])
+    return possible_pathotypes, list(set(genes_present))
+
+
+module_timer = functools.partial(utils.timer, name='Module Typing')
+
+
+@module_timer
+def typing(data_by_gene, typing_rules_file, min_gene_coverage, min_gene_identity, min_gene_depth, outdir):
+    possible_pathotypes, genes_present = possible_types(data_by_gene, typing_rules_file, min_gene_coverage,
+                                                        min_gene_identity, min_gene_depth)
+    with open(os.path.join(outdir, 'patho_typing.report.txt'), 'wt') as writer_report:
+        with open(os.path.join(outdir, 'patho_typing.extended_report.txt'), 'wt') as writer_extended_report:
+            writer_extended_report.write('#Pathotypes_found' + '\n')
+            if len(possible_pathotypes) > 0:
+                writer_report.write('\n'.join(possible_pathotypes) + '\n')
+                writer_extended_report.write('\n'.join(possible_pathotypes) + '\n')
+                print('\n' + 'Pathotypes found:' + '\n')
+                print('\n'.join(possible_pathotypes) + '\n')
+            else:
+                writer_report.write('TND' + '\n')  # Type Not Determined
+                writer_extended_report.write('TND' + '\n')  # Type Not Determined
+                print('\n' + 'It was not possible to identify any possible pathotype match' + '\n')
+            writer_extended_report.write('\n' + '#Genes_present' + '\n')
+            writer_extended_report.write('\n'.join(genes_present) + '\n')
+
+    return None, None

scripts/modules/utils.py

diff -r 000000000000 -r 8be2feb96994 scripts/modules/utils.py

scripts/modules/utils.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/modules/utils.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,370 @@
+import pickle
+import traceback
+import shlex
+import subprocess
+from threading import Timer
+import shutil
+import time
+import functools
+import os.path
+import sys
+import argparse
+
+
+def start_logger(workdir):
+    time_str = time.strftime("%Y%m%d-%H%M%S")
+    sys.stdout = Logger(workdir, time_str)
+    logfile = sys.stdout.getLogFile()
+    return logfile, time_str
+
+
+class Logger(object):
+    def __init__(self, out_directory, time_str):
+        self.logfile = os.path.join(out_directory, str('run.' + time_str + '.log'))
+        self.terminal = sys.stdout
+        self.log = open(self.logfile, "w")
+
+    def write(self, message):
+        self.terminal.write(message)
+        self.log.write(message)
+        self.log.flush()
+
+    def flush(self):
+        pass
+
+    def getLogFile(self):
+        return self.logfile
+
+
+def checkPrograms(programs_version_dictionary):
+    print('\n' + 'Checking dependencies...')
+    programs = programs_version_dictionary
+    which_program = ['which', '']
+    listMissings = []
+    for program in programs:
+        which_program[1] = program
+        run_successfully, stdout, stderr = runCommandPopenCommunicate(which_program, False, None, False)
+        if not run_successfully:
+            listMissings.append(program + ' not found in PATH.')
+        else:
+            print(stdout.splitlines()[0])
+            if programs[program][0] is None:
+                print(program + ' (impossible to determine programme version) found at: ' + stdout.splitlines()[0])
+            else:
+                if program.endswith('.jar'):
+                    check_version = ['java', '-jar', stdout.splitlines()[0], programs[program][0]]
+                    programs[program].append(stdout.splitlines()[0])
+                else:
+                    check_version = [stdout.splitlines()[0], programs[program][0]]
+                run_successfully, stdout, stderr = runCommandPopenCommunicate(check_version, False, None, False)
+                if stdout == '':
+                    stdout = stderr
+                if program in ['wget', 'awk']:
+                    version_line = stdout.splitlines()[0].split(' ', 3)[2]
+                elif program in ['prefetch', 'fastq-dump']:
+                    version_line = stdout.splitlines()[1].split(' ')[-1]
+                else:
+                    version_line = stdout.splitlines()[0].split(' ')[-1]
+                replace_characters = ['"', 'v', 'V', '+', ',']
+                for i in replace_characters:
+                    version_line = version_line.replace(i, '')
+                print(program + ' (' + version_line + ') found')
+                if programs[program][1] == '>=':
+                    program_found_version = version_line.split('.')
+                    program_version_required = programs[program][2].split('.')
+                    if len(program_version_required) == 3:
+                        if len(program_found_version) == 2:
+                            program_found_version.append(0)
+                        else:
+                            program_found_version[2] = program_found_version[2].split('_')[0]
+                    for i in range(0, len(program_version_required)):
+                        if int(program_found_version[i]) > int(program_version_required[i]):
+                            break
+                        elif int(program_found_version[i]) == int(program_version_required[i]):
+                            continue
+                        else:
+                            listMissings.append('It is required ' + program + ' with version ' +
+                                                programs[program][1] + ' ' + programs[program][2])
+                else:
+                    if version_line != programs[program][2]:
+                        listMissings.append('It is req..    if len(values) not in tuple_length_options:
+                msg = 'Option {argument_name} requires one of the following number of' \
+                      ' arguments: {tuple_length_options}'.format(argument_name=self.argument_name,
+                                                                  tuple_length_options=tuple_length_options)
+                raise argparse.ArgumentTypeError(msg)
+            setattr(args, self.dest, values)
+    return RequiredLength
+
+
+def get_sequence_information(fasta_file, length_extra_seq):
+    sequence_dict = {}
+    headers = {}
+
+    with open(fasta_file, 'rtU') as reader:
+        blank_line_found = False
+        sequence_counter = 0
+        temp_sequence_dict = {}
+        for line in reader:
+            line = line.splitlines()[0]
+            if len(line) > 0:
+                if not blank_line_found:
+                    if line.startswith('>'):
+                        if len(temp_sequence_dict) > 0:
+                            if list(temp_sequence_dict.values())[0]['length'] - 2 * length_extra_seq > 0:
+                                sequence_dict[list(temp_sequence_dict.keys())[0]] = list(temp_sequence_dict.values())[0]
+                                headers[list(temp_sequence_dict.values())[0]['header'].lower()] = sequence_counter
+                            else:
+                                print(list(temp_sequence_dict.values())[0]['header'] + ' sequence ignored due to '
+                                                                                       'length <= 0')
+                            temp_sequence_dict = {}
+
+                        if line[1:].lower() in headers:
+                            sys.exit('Found duplicated sequence headers')
+
+                        sequence_counter += 1
+                        temp_sequence_dict[sequence_counter] = {'header': line[1:].lower(), 'sequence': '', 'length': 0}
+                    else:
+                        temp_sequence_dict[sequence_counter]['sequence'] += line.upper()
+                        temp_sequence_dict[sequence_counter]['length'] += len(line)
+                else:
+                    sys.exit('It was found a blank line between the fasta file above line ' + line)
+            else:
+                blank_line_found = True
+
+        if len(temp_sequence_dict) > 0:
+            if list(temp_sequence_dict.values())[0]['length'] - 2 * length_extra_seq > 0:
+                sequence_dict[list(temp_sequence_dict.keys())[0]] = list(temp_sequence_dict.values())[0]
+                headers[list(temp_sequence_dict.values())[0]['header'].lower()] = sequence_counter
+            else:
+                print(list(temp_sequence_dict.values())[0]['header'] + ' sequence ignored due to length <= 0')
+
+    return sequence_dict, headers
+
+
+def simplify_sequence_dict(sequence_dict):
+    simple_sequence_dict = {}
+    for counter, info in list(sequence_dict.items()):
+        simple_sequence_dict[info['header']] = info
+        del simple_sequence_dict[info['header']]['header']
+    return simple_sequence_dict
+
+
+def chunkstring(string, length):
+    return (string[0 + i:length + i] for i in range(0, len(string), length))
+
+
+def clean_headers_sequences(sequence_dict):
+    problematic_characters = ["|", " ", ",", ".", "(", ")", "'", "/", ":"]
+    # print 'Checking if reference sequences contain ' + str(problematic_characters) + '\n'
+
+    headers_changed = False
+    new_headers = {}
+    for i in sequence_dict:
+        if any(x in sequence_dict[i]['header'] for x in problematic_characters):
+            for x in problematic_characters:
+                sequence_dict[i]['header'] = sequence_dict[i]['header'].replace(x, '_')
+            headers_changed = True
+        new_headers[sequence_dict[i]['header'].lower()] = i
+
+    if headers_changed:
+        print('At least one of the those characters was found. Replacing those with _' + '\n')
+
+    return sequence_dict, new_headers

scripts/patho_typing.pl

diff -r 000000000000 -r 8be2feb96994 scripts/patho_typing.pl

scripts/patho_typing.pl

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/patho_typing.pl Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,60 @@
+#!/usr/bin/env perl
+## A wrapper script to collect patho_typing.py output
+use strict;
+use warnings;
+use Cwd;
+use English;
+use File::Copy;
+use File::Basename;
+
+# Parse arguments
+my ($python) = @ARGV;
+
+# Run program
+runPathoTyping();
+collectOutput();
+exit 0;
+
+# Run patho_typing
+sub runPathoTyping {
+    my $abs_path = Cwd::abs_path($PROGRAM_NAME);
+    my $scriptdir = dirname($abs_path);
+    my $rematchdir = "$scriptdir/ReMatCh";
+    my $newpath = "PATH=$ENV{PATH}:$rematchdir";
+    `$newpath; $python`;
+     return 0;
+}
+
+sub collectOutput{
+    my $patho_type = "";
+    open(my $fh, '<', 'output_dir/rematch/rematchModule_report.txt') || die "Could not open file 'output_dir/rematch/rematchModule_report.txt' $!";
+    my @rematch_lines = <$fh>;
+    close($fh);
+    my @rematch_table = "";
+    my @rematch_total_table = "";
+    my $highest_coverage = 0;
+    foreach(@rematch_lines) {
+      if ($_ =~ m/\t/) { # Only table lines
+        my @elems = split('\t', $_);
+        if ($_ =~ m/#/) { # First line
+          s/_/ /g for @elems;
+          push(@rematch_table,join("\t", @elems[0,1,2,5]));
+          push(@rematch_total_table,join("\t", @elems[0,1,2,5]));
+        }
+        else {
+          push(@rematch_total_table,join("\t", @elems[0,1,2,5]));
+          if ($elems[1] > 90.0) { # Only genes with over 90% coverage in report table
+            push(@rematch_table,join("\t", @elems[0,1,2,5]));
+          }
+        }
+      }
+    }
+    open($fh, '>', 'pathotyper_rep_tab') || die "Could not open file 'pathotyper_rep_tab' $!";
+    print $fh @rematch_table;
+    close($fh);
+    open($fh, '>', 'pathotyper_rep_tot_tab') || die "Could not open file 'pathotyper_rep_tot_tab' $!";
+    print $fh @rematch_total_table;
+    close($fh);
+
+    return 0;
+}

scripts/patho_typing.py

diff -r 000000000000 -r 8be2feb96994 scripts/patho_typing.py

scripts/patho_typing.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/patho_typing.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,482 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+"""
+patho_typing.py - In silico pathogenic typing directly from raw
+Illumina reads
+<https://github.com/B-UMMI/patho_typing/>
+
+Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+
+Last modified: October 15, 2018
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+2020-01-13 ISS
+In order to use the module within the EURL_WGS_Typer pipeline with a
+different virulence database for E coli, mapping against the
+typing_rules.tab was deactivated.
+"""
+
+import argparse
+import os
+import time
+import sys
+from pkg_resources import resource_filename
+
+try:
+    from __init__ import __version__
+
+    import modules.utils as utils
+    import modules.run_rematch as run_rematch
+    import modules.typing as typing
+except ImportError:
+    from pathotyping.__init__ import __version__
+
+    from pathotyping.modules import utils as utils
+    from pathotyping.modules import run_rematch as run_rematch
+    from pathotyping.modules import typing as typing
+
+
+def set_reference(species, outdir, script_path, trueCoverage):
+    reference_file = None
+    trueCoverage_file = None
+    trueCoverage_sequences = None
+    trueCoverage_headers = None
+    trueCoverage_config = None
+    typing_file = None
+    typing_sequences = None
+    typing_headers = None
+    typing_rules = None
+    typing_config = None
+
+    species_folder = os.path.join(os.path.dirname(script_path), 'modules', 'seq_conf',
+                                  '_'.join([s.lower() for s in species]), '')
+
+    if os.path.isdir(species_folder):
+        typing_rules = os.path.join(species_folder, 'typing_rules.tab')
+        typing_file = os.path.join(species_folder, 'typing.fasta')
+        typing_sequences, ignore = utils.get_sequence_information(typing_file, 0)
+        typing_sequences, typing_headers = utils.clean_headers_sequences(typing_sequences)
+        typing_sequences = utils.simplify_sequence_dict(typing_sequences)
+        typing_config = os.path.join(species_folder, 'typing.config')
+        if trueCoverage:
+            if os.path.isfile(os.path.join(species_folder, 'trueCoverage.fasta')):
+                trueCoverage_file = os.path.join(species_folder, 'trueCoverage.fasta')
+                trueCoverage_sequences, ignore = utils.get_sequence_information(trueCoverage_file, 0)
+                trueCoverage_sequences, trueCoverage_headers = utils.clean_headers_sequences(trueCoverage_sequences)
+                trueCoverage_sequences = utils.simplify_sequence_dict(trueCoverage_sequences)
+                trueCoverage_config = os.path.join(species_folder, 'trueCoverage.config')
+
+                trueCoverage_typing_sequences = trueCoverage_sequences.copy()
+                for header in typing_sequences:
+                    if header not in trueCoverage_sequences:
+                        trueCoverage_typing_sequences[header] = typing_sequences[header]
+                    else:
+                        print('Sequence {header} of typing.fasta already present in'
+                              ' trueCoverage.fasta'.format(header=header))
+
+                reference_file = os.path.join(outdir, 'trueCoverage_typing.fasta')
+                write_sequeces(reference_file, trueCoverage_typing_seq.. print('\n' + e + '\n')
+                                if not args.noCheckPoint:
+                                    clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+                                    _ = utils.runTime(start_time)
+                                    sys.exit(e)
+                        else:
+                            e = 'TrueCoverage module did not run successfully'
+                            print('\n' + e + '\n')
+                            if not args.noCheckPoint:
+                                clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+                                _ = utils.runTime(start_time)
+                                sys.exit(e)
+
+                        print('\n')
+                        typing_dir = os.path.join(rematch_dir, 'typing', '')
+                        if not os.path.isdir(typing_dir):
+                            os.makedirs(typing_dir)
+                        run_successfully, bam_file = split_bam(bam_file, typing_headers, typing_dir, args.threads)
+                        if run_successfully:
+                            run_successfully = indexAlignment(bam_file)
+                            if run_successfully:
+                                reference_file = os.path.join(typing_dir, 'reference.fasta')
+                                write_sequeces(reference_file, typing_sequences)
+                                index_fasta_samtools(reference_file, None, None, True)
+                                rematch_dir = str(typing_dir)
+                if not run_successfully:
+                    if args.noCheckPoint:
+                        clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+                        _ = utils.runTime(start_time)
+                        sys.exit('Something in the required TrueCoverage analysis went wrong')
+            else:
+                print('\n'
+                      'WARNING: it was not found trueCoverage target files. trueCoverage will not run.'
+                      '\n')
+
+        if run_successfully:
+            config = parse_config(typing_config)
+            if args.minGeneCoverage is not None:
+                config['minimum_gene_coverage'] = args.minGeneCoverage
+            if args.minGeneIdentity is not None:
+                config['minimum_gene_identity'] = args.minGeneIdentity
+
+            runtime, run_successfully, sample_data_general, data_by_gene = \
+                run_rematch.run_rematch(rematch, rematch_dir, reference_file, bam_file, args.threads,
+                                        config['length_extra_seq'], config['minimum_depth_presence'],
+                                        config['minimum_depth_call'], config['minimum_depth_frequency_dominant_allele'],
+                                        config['minimum_gene_coverage'], config['minimum_gene_identity'],
+                                        args.debug, args.doNotRemoveConsensus)
+            if run_successfully and data_by_gene is not None:
+                if args.minGeneDepth is None:
+                    args.minGeneDepth = sample_data_general['mean_sample_coverage'] / 3 if \
+                                        sample_data_general['mean_sample_coverage'] / 3 > 15 else \
+                                        15
+            else:
+                clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+                _ = utils.runTime(start_time)
+                sys.exit('ReMatCh run for pathotyping did not run successfully')
+        else:
+            clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+            _ = utils.runTime(start_time)
+            sys.exit('Something did not run successfully')
+
+    clean_pathotyping_folder(args.outdir, original_reference_file, args.debug)
+
+    print('\n')
+    _ = utils.runTime(start_time)
+
+
+if __name__ == "__main__":
+    main()

scripts/rgFastQC.py

diff -r 000000000000 -r 8be2feb96994 scripts/rgFastQC.py

scripts/rgFastQC.py

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/rgFastQC.py Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,162 @@
+"""
+Rewrite of rgFastQC.py for Version 0.11.2 of FastQC.
+
+Changes implemented from tmcgowan at
+https://testtoolshed.g2.bx.psu.edu/view/tmcgowan/fastqc
+and iuc at https://toolshed.g2.bx.psu.edu/view/iuc/fastqc
+with minor changes and bug fixes
+
+SYNOPSIS
+
+    rgFastQC.py -i input_file -j input_file.name -o output_html_file [-d output_directory]
+        [-f fastq|bam|sam] [-n job_name] [-c contaminant_file] [-e fastqc_executable]
+
+EXAMPLE (generated by Galaxy)
+
+    rgFastQC.py -i path/dataset_1.dat -j 1000gsample.fastq -o path/dataset_3.dat -d path/job_working_directory/subfolder
+        -f fastq -n FastQC -c path/dataset_2.dat -e fastqc
+
+"""
+
+import re
+import os
+import shutil
+import subprocess
+import optparse
+import tempfile
+import glob
+import gzip
+import bz2
+import zipfile
+
+class FastQCRunner(object):
+
+    def __init__(self,opts=None):
+        '''
+        Initializes an object to run FastQC in Galaxy. To start the process, use the function run_fastqc()
+        '''
+
+        # Check whether the options are specified and saves them into the object
+        assert opts != None
+        self.opts = opts
+
+    def prepare_command_line(self):
+        '''
+        Develops the Commandline to run FastQC in Galaxy
+        '''
+
+        # Check whether a given file compression format is valid
+        # This prevents uncompression of already uncompressed files
+        infname = self.opts.inputfilename
+        linf = infname.lower()
+        trimext = False
+        # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
+        # patched may 29 2013 until this is fixed properly
+        if ( linf.endswith('.gz') or linf.endswith('.gzip') ):
+            f = gzip.open(self.opts.input)
+            try:
+                f.readline()
+            except:
+                trimext = True
+            f.close()
+        elif linf.endswith('bz2'):
+            f = bz2.open(self.opts.input,'rb')
+            try:
+                f.readline()
+            except:
+                trimext = True
+            f.close()
+        elif linf.endswith('.zip'):
+            if not zipfile.is_zipfile(self.opts.input):
+                trimext = True
+        if trimext:
+            f = open(self.opts.input)
+            try:
+                f.readline()
+            except:
+                raise Exception("Input file corruption, could not identify the filetype")
+                infname = os.path.splitext(infname)[0]
+
+        # Replace unwanted or problematic charaters in the input file name
+        self.fastqinfilename = re.sub(r'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
+        # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise
+        if 'fastq' in opts.informat:
+            # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's
+            # accepted formats..
+            opts.informat = 'fastq'
+        elif not self.fastqinfilename.endswith(opts.informat):
+            self.fastqinfilename += '.%s' % opts.informat
+
+        # Build the Commandline from the given parameters
+        command_line = [opts.executable, '--outdir %s' % opts.outputdir]
+        if opts.contaminants != None:
+            command_line.append('--contaminants %s' % opts.contaminants)
+        if opts.limits != None:
+            command_line.append('--limits %s' % opts.limits)
+        command_line.append('--quiet')
+        command_line.append('--extract') # to access the output text file
+        command_line.append(self.fastqinfilename)
+        command_line.append('-f %s' % opts.informat)
+        self.command_line = ' '.join(command_line)
+
+    def copy_output_file_to_dataset(self):
+        '''
+        Retrieves the output html and text files from the output directory and copies them to the Galaxy output files
+        '''
+
+        # retrieve html file
+        result_file = glob.glob(opts.outputdir + '/*html')
+        with open(result_file[0], 'rb') as fsrc:
+            with open(self.opts.htmloutput, 'wb') as fdest:
+                shutil.copyfileobj(fsrc, fdest)
+
+        # retrieve text file
+        text_file = glob.glob(opts.outputdir + '/*/fastqc_data.txt')
+        with open(text_file[0], 'rb') as fsrc:
+            with open(self.opts.textoutput, 'wb') as fdest:
+                shutil.copyfileobj(fsrc, fdest)
+
+    def run_fastqc(self):
+        '''
+        Executes FastQC. Make sure the mandatory import parameters input, inputfilename, outputdir and htmloutput have been specified in the options (opts)
+        '''
+
+        # Create a log file
+        dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir)
+        sout = open(tlog, 'w')
+
+        self.prepare_command_line()
+        sout.write(self.command_line)
+        sout.write('\n')
+        sout.write("Creating symlink\n") # between the input (.dat) file and the given input file name
+        os.symlink(self.opts.input, self.fastqinfilename)
+        sout.write("check_call\n")
+        subprocess.check_call(self.command_line, shell=True)
+        sout.write("Copying working %s file to %s \n" % (self.fastqinfilename, self.opts.htmloutput))
+        self.copy_output_file_to_dataset()
+        sout.write("Finished")
+        sout.close()
+
+if __name__ == '__main__':
+    op = optparse.OptionParser()
+    op.add_option('-i', '--input', default=None)
+    op.add_option('-j', '--inputfilename', default=None)
+    op.add_option('-o', '--htmloutput', default=None)
+    op.add_option('-t', '--textoutput', default=None)
+    op.add_option('-d', '--outputdir', default="/tmp/shortread")
+    op.add_option('-f', '--informat', default='fastq')
+    op.add_option('-n', '--namejob', default='rgFastQC')
+    op.add_option('-c', '--contaminants', default=None)
+    op.add_option('-l', '--limits', default=None)
+    op.add_option('-e', '--executable', default='fastqc')
+    opts, args = op.parse_args()
+
+    assert opts.input != None
+    assert opts.inputfilename != None
+    assert opts.htmloutput != None
+    #assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable
+    if not os.path.exists(opts.outputdir):
+        os.makedirs(opts.outputdir)
+
+    fastqc_runner = FastQCRunner(opts)
+    fastqc_runner.run_fastqc()

scripts/spades.pl

diff -r 000000000000 -r 8be2feb96994 scripts/spades.pl

scripts/spades.pl

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/spades.pl Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,133 @@
+#!/usr/bin/env perl
+## A wrapper script to call spades.py and collect its output
+use strict;
+use warnings;
+use File::Temp qw/ tempfile tempdir /;
+use File::Copy;
+use Getopt::Long;
+
+# Parse arguments
+my ($out_contigs_file,
+    $out_contigs_stats,
+    $out_scaffolds_file,
+    $out_scaffolds_stats,
+    $out_log_file,
+    $new_name,
+    @sysargs) = @ARGV;
+
+## GetOptions not compatible with parsing the rest of the arguments in an array.
+## Keeping the not-so-nice parse-in-one-go method, without named arguments.
+# GetOptions(
+#     'contigs-file=s'    => \$out_contigs_file,
+#     'contigs-stats=s'   => \$out_contigs_stats,
+#     'scaffolds-file=s'  => \$out_scaffolds_file,
+#     'scaffolds-stats=s' => \$out_scaffolds_stats,
+#     'out_log_file=s'    => \$out_log_file,
+# );
+
+# my @sysargs = @ARGV;
+
+# Create temporary folder to store files, delete after use
+#my $output_dir = tempdir( CLEANUP => 0 );
+my $output_dir = 'output_dir';
+# Link "dat" files as fastq, otherwise spades complains about file format
+
+# Create log handle
+open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n";
+
+# Run program
+# To do: record time
+runSpades(@sysargs);
+collectOutput($new_name);
+extractCoverageLength($out_contigs_file, $out_contigs_stats);
+extractCoverageLength($out_scaffolds_file, $out_scaffolds_stats);
+print $log "Done\n";
+close $log;
+exit 0;
+
+# Run spades
+sub runSpades {
+    my $cmd = join(" ", @_) . " -o $output_dir";
+    my $return_code = system($cmd);
+    if ($return_code) {
+ print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
+ die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
+    }
+    return 0;
+}
+
+# Collect output
+sub collectOutput{
+    my ($new_name) = @_;
+
+    # Collects output
+    #if a new name is given for the contigs and scaffolds, change them before moving them
+    if ( $new_name ne 'NODE') {
+        renameContigs($new_name);
+    }
+    else {
+        if ( -e "$output_dir/contigs.fasta") {
+            move "$output_dir/contigs.fasta", $out_contigs_file;
+        }
+        if ( -e "$output_dir/scaffolds.fasta") {
+            move "$output_dir/scaffolds.fasta", $out_scaffolds_file;
+        }
+    }
+
+    open LOG, '<', "$output_dir/spades.log"
+ or die "Cannot open log file $output_dir/spades.log: $?";
+    print $log $_ while (<LOG>);
+    return 0;
+}
+
+#Change name in contig and scaffolds file
+sub renameContigs{
+    my ($name) = @_;
+
+    open my $in, '<',"$output_dir/contigs.fasta" or die $!;
+    open my $out,'>', $out_contigs_file;
+
+    while ( my $line = <$in>) {
+        #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
+        #also move the remainder of the length
+        if ( $line =~ />NODE_(\d+)_(.+)/) {
+            $line = ">$name" . "_$1 $2\n";
+        }
+        print $out $line;
+    }
+    close $in;
+    close $out;
+
+
+    open $in, '<',"$output_dir/scaffolds.fasta" or die $!;
+    open $out,'>', $out_scaffolds_file;
+
+    while ( my $line = <$in>) {
+        #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
+        #also move the remainder of the length
+        if ( $line =~ />NODE_(\d+)_(.+)/) {
+            $line = ">$name" . "_$1 $2\n";
+        }
+        print $out $line;
+    }
+    close $in;
+    close $out;
+
+}
+
+
+# Extract
+sub extractCoverageLength{
+    my ($in, $out) = @_;
+    open FASTA, '<', $in or die $!;
+    open TAB, '>', $out or die $!;
+    print TAB "#name\tlength\tcoverage\n";
+    while (<FASTA>){
+ next unless /^>/;
+ chomp;
+ die "Not all elements found in $_\n" if (! m/^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)/);
+ my ($name,$n, $l, $cov) = ($1,$2, $3, $4);
+ print TAB "$name" . "_$n\t$l\t$cov\n";
+    }
+    close TAB;
+}

scripts/stx_subtype_fa.sh

diff -r 000000000000 -r 8be2feb96994 scripts/stx_subtype_fa.sh

scripts/stx_subtype_fa.sh

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/stx_subtype_fa.sh Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,7 @@
+tooldir="$1";
+fastafile="$2";
+
+# SEQUENCE SEARCH
+blastn -query $fastafile -db $tooldir/data/stx -task blastn -evalue 0.001 -out shigatoxin -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+# SHIGATOXINTYPER: FILTER, CUT AND CONCATENATE SEQUENCE SEARCH OUTPUT
+awk -F '\t' '($3>95 && $4>1200) { print $2 FS $3 FS $4 FS $16 }' shigatoxin > shigatoxin_fc;
\ No newline at end of file

scripts/stx_subtype_pe.sh

diff -r 000000000000 -r 8be2feb96994 scripts/stx_subtype_pe.sh

data/stx.fa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/stx_subtype_pe.sh Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,80 @@
+tooldir="$1";
+fastqfile1="$2";
+fastqfile2="$3";
+fastafile="$4";
+
+# ASSEMBLY
+mkdir stxdir;
+skesa --fastq $fastqfile1 $fastqfile2 --contigs_out stxdir/skesa.fasta;
+cp $fastafile stxdir/spades.fasta;
+rm -r output_dir;
+
+# FILTER + ASSEMBLY
+$tooldir/scripts/duk -m stxdir/filtered1STX.fq -k 23 $tooldir/data/stx.fa $fastqfile1;
+$tooldir/scripts/duk -m stxdir/filtered2STX.fq -k 23 $tooldir/data/stx.fa $fastqfile2;
+$tooldir/scripts/fastq_pair stxdir/filtered1STX.fq stxdir/filtered2STX.fq;
+$tooldir/scripts/fastq_pair stxdir/filtered1STX.fq.single.fq $fastqfile2;
+$tooldir/scripts/fastq_pair stxdir/filtered2STX.fq.single.fq $fastqfile1;
+cat stxdir/filtered1STX.fq.paired.fq > stxdir/filtered1STX_paired.fq;
+cat stxdir/filtered1STX.fq.single.fq.paired.fq >> stxdir/filtered1STX_paired.fq;
+cat trimmed1.paired.fq >> stxdir/filtered1STX_paired.fq;
+cat stxdir/filtered2STX.fq.paired.fq > stxdir/filtered2STX_paired.fq;
+cat trimmed2.paired.fq >> stxdir/filtered2STX_paired.fq;
+cat stxdir/filtered2STX.fq.single.fq.paired.fq >> stxdir/filtered2STX_paired.fq;
+dukstx1filesize=$(wc -c "stxdir/filtered1STX_paired.fq" | awk '{print $1}');
+dukstx2filesize=$(wc -c "stxdir/filtered2STX_paired.fq" | awk '{print $1}');
+if [ $dukstx1filesize -gt 0 ] && [ $dukstx2filesize -gt 0 ]
+then
+  skesa --fastq stxdir/filtered1STX_paired.fq stxdir/filtered2STX_paired.fq --contigs_out stxdir/duk_skesa.fasta;
+  perl $tooldir/scripts/spades.pl duk_spades_contigs duk_spades_contig_stats duk_spades_scaffolds duk_spades_scaffold_stats duk_spades_log NODE spades.py --disable-gzip-output --isolate -t 8 --pe1-ff --pe1-1 stxdir/filtered1STX_paired.fq --pe1-2 stxdir/filtered2STX_paired.fq
+  mv duk_spades_contigs stxdir/duk_spades.fasta;
+  rm -r output_dir;
+  blastn -query stxdir/duk_skesa.fasta -db $tooldir/data/stx -task blastn -evalue 0.001 -out stxdir/duk_skesa_seqs -outfmt '6 qseqid sseqid sframe qseq' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+  blastn -query stxdir/duk_spades.fasta -db $tooldir/data/stx -task blastn -evalue 0.001 -out stxdir/duk_spades_seqs -outfmt '6 qseqid sseqid sframe qseq' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+else
+  touch stxdir/duk_skesa_seqs;
+  touch stxdir/duk_spades_seqs;
+fi
+
+# SEQUENCE SEARCH
+blastn -query stxdir/skesa.fasta -db $tooldir/data/stx -task blastn -evalue 0.001 -out stxdir/skesa_seqs -outfmt '6 qseqid sseqid sframe qseq' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+blastn -query stxdir/spades.fasta -db $tooldir/data/stx -task blastn -evalue 0.001 -out stxdir/spades_seqs -outfmt '6 qseqid sseqid sframe qseq' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+# DIVIDE STX1 FROM STX2
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx1") print $1,$3,$4}' stxdir/skesa_seqs > stxdir/stx1_skesa_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx2") print $1,$3,$4}' stxdir/skesa_seqs > stxdir/stx2_skesa_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx1") print $1,$3,$4}' stxdir/duk_skesa_seqs > stxdir/dukstx1_skesa_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx2") print $1,$3,$4}' stxdir/duk_skesa_seqs > stxdir/dukstx2_skesa_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx1") print $1,$3,$4}' stxdir/spades_seqs > stxdir/stx1_spades_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx2") print $1,$3,$4}' stxdir/spades_seqs > stxdir/stx2_spades_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx1") print $1,$3,$4}' stxdir/duk_spades_seqs > stxdir/dukstx1_spades_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx2") print $1,$3,$4}' stxdir/duk_spades_seqs > stxdir/dukstx2_spades_seqs;
+# CREATE COMBINED MULTIFASTA FROM SEQUENCES
+perl $tooldir/scripts/MultifastaFromBlast.pl "stxdir/stx1_skesa_seqs,stxdir/dukstx1_skesa_seqs,stxdir/stx1_spades_seqs,stxdir/dukstx1_spades_seqs" "stxdir/multiassembly_stx1.fasta";
+perl $tooldir/scripts/MultifastaFromBlast.pl "stxdir/stx2_skesa_seqs,stxdir/dukstx2_skesa_seqs,stxdir/stx2_spades_seqs,stxdir/dukstx2_spades_seqs" "stxdir/multiassembly_stx2.fasta";
+
+# ALIGN AND GET CONSENSUS
+stx1filesize=$(wc -c "stxdir/multiassembly_stx1.fasta" | awk '{print $1}');
+if [ $stx1filesize -eq 0 ]
+then
+  touch stxdir/multiassembly_stx1_consensus.fasta;
+else
+  cat $tooldir/data/stx1.fa >> stxdir/multiassembly_stx1.fasta;
+  muscle -in stxdir/multiassembly_stx1.fasta -out stxdir/multiassembly_stx1_aligned.fasta;
+  awk 'BEGIN {RS=">" ; ORS=""} substr($1,1,4)!="stx1" {print ">"$0}' stxdir/multiassembly_stx1_aligned.fasta > stxdir/multiassembly_stx1_aligned_clean.fasta;
+  awk '/^>/ {printf("%s%s\n",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' stxdir/multiassembly_stx1_aligned_clean.fasta > stxdir/multiassembly_stx1_aligned_linear.fasta;
+  python $tooldir/scripts/GetConsensus.py -i stxdir/multiassembly_stx1_aligned_linear.fasta -o stxdir/multiassembly_stx1_consensus.fasta;
+fi
+
+stx2filesize=$(wc -c "stxdir/multiassembly_stx2.fasta" | awk '{print $1}');
+if [ $stx2filesize -eq 0 ]
+then
+  touch stxdir/multiassembly_stx2_consensus.fasta;
+else
+  cat $tooldir/data/stx2.fa >> stxdir/multiassembly_stx2.fasta;
+  muscle -in stxdir/multiassembly_stx2.fasta -out stxdir/multiassembly_stx2_aligned.fasta;
+  awk 'BEGIN {RS=">" ; ORS=""} substr($1,1,4)!="stx2" {print ">"$0}' stxdir/multiassembly_stx2_aligned.fasta > stxdir/multiassembly_stx2_aligned_clean.fasta;
+  awk '/^>/ {printf("%s%s\n",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' stxdir/multiassembly_stx2_aligned_clean.fasta > stxdir/multiassembly_stx2_aligned_linear.fasta;
+  python $tooldir/scripts/GetConsensus.py -i stxdir/multiassembly_stx2_aligned_linear.fasta -o stxdir/multiassembly_stx2_consensus.fasta;
+fi
+cat stxdir/multiassembly_stx1_consensus.fasta > stx.fasta;
+cat stxdir/multiassembly_stx2_consensus.fasta >> stx.fasta;

scripts/stx_subtype_se.sh

diff -r 000000000000 -r 8be2feb96994 scripts/stx_subtype_se.sh

data/stx.fa

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/stx_subtype_se.sh Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,68 @@
+tooldir="$1";
+fastqfile="$2";
+fastafile="$3";
+
+# ASSEMBLY
+mkdir stxdir;
+skesa --fastq $fastqfile --contigs_out stxdir/skesa.fasta;
+cp $fastafile stxdir/spades.fasta;
+rm -r output_dir;
+
+# FILTER + ASSEMBLY
+$tooldir/scripts/duk -m stxdir/duk.fq -k 23 $tooldir/data/stx.fa $fastqfile;
+dukfilesize=$(wc -c "stxdir/duk.fq" | awk '{print $1}');
+if [ $dukfilesize -gt 0 ]
+then
+  skesa --fastq stxdir/duk.fq --contigs_out stxdir/duk_skesa.fasta;
+  perl $tooldir/scripts/spades.pl duk_spades_contigs duk_spades_contig_stats duk_spades_scaffolds duk_spades_scaffold_stats duk_spades_log NODE spades.py --disable-gzip-output --isolate -t 8 --iontorrent -s stxdir/duk.fq;
+  mv duk_spades_contigs stxdir/duk_spades.fasta;
+  rm -r output_dir;
+  blastn -query stxdir/duk_skesa.fasta -db $tooldir/data/stx -task blastn -evalue 0.001 -out stxdir/duk_skesa_seqs -outfmt '6 qseqid sseqid sframe qseq' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+  blastn -query stxdir/duk_spades.fasta -db $tooldir/data/stx -task blastn -evalue 0.001 -out stxdir/duk_spades_seqs -outfmt '6 qseqid sseqid sframe qseq' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+else
+  touch stxdir/duk_skesa_seqs;
+  touch stxdir/duk_spades_seqs;
+fi
+
+# SEQUENCE SEARCH
+blastn -query stxdir/skesa.fasta -db $tooldir/data/stx -task blastn -evalue 0.001 -out stxdir/skesa_seqs -outfmt '6 qseqid sseqid sframe qseq' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+blastn -query stxdir/spades.fasta -db $tooldir/data/stx -task blastn -evalue 0.001 -out stxdir/spades_seqs -outfmt '6 qseqid sseqid sframe qseq' -num_threads 8 -strand both -dust yes -max_target_seqs 1 -perc_identity 95.0;
+# DIVIDE STX1 FROM STX2
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx1") print $1,$3,$4}' stxdir/skesa_seqs > stxdir/stx1_skesa_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx2") print $1,$3,$4}' stxdir/skesa_seqs > stxdir/stx2_skesa_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx1") print $1,$3,$4}' stxdir/duk_skesa_seqs > stxdir/dukstx1_skesa_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx2") print $1,$3,$4}' stxdir/duk_skesa_seqs > stxdir/dukstx2_skesa_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx1") print $1,$3,$4}' stxdir/spades_seqs > stxdir/stx1_spades_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx2") print $1,$3,$4}' stxdir/spades_seqs > stxdir/stx2_spades_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx1") print $1,$3,$4}' stxdir/duk_spades_seqs > stxdir/dukstx1_spades_seqs;
+awk 'BEGIN { OFS="\t" }!seen[$1]++ {if (substr($2,1,4)=="stx2") print $1,$3,$4}' stxdir/duk_spades_seqs > stxdir/dukstx2_spades_seqs;
+# CREATE COMBINED MULTIFASTA FROM SEQUENCES
+perl $tooldir/scripts/MultifastaFromBlast.pl "stxdir/stx1_skesa_seqs,stxdir/dukstx1_skesa_seqs,stxdir/stx1_spades_seqs,stxdir/dukstx1_spades_seqs" "stxdir/multiassembly_stx1.fasta";
+perl $tooldir/scripts/MultifastaFromBlast.pl "stxdir/stx2_skesa_seqs,stxdir/dukstx2_skesa_seqs,stxdir/stx2_spades_seqs,stxdir/dukstx2_spades_seqs" "stxdir/multiassembly_stx2.fasta";
+
+# ALIGN AND GET CONSENSUS
+stx1filesize=$(wc -c "stxdir/multiassembly_stx1.fasta" | awk '{print $1}');
+if [ $stx1filesize -eq 0 ]
+then
+  touch stxdir/multiassembly_stx1_consensus.fasta;
+else
+  cat $tooldir/data/stx1.fa >> stxdir/multiassembly_stx1.fasta;
+  muscle -in stxdir/multiassembly_stx1.fasta -out stxdir/multiassembly_stx1_aligned.fasta;
+  awk 'BEGIN {RS=">" ; ORS=""} substr($1,1,4)!="stx1" {print ">"$0}' stxdir/multiassembly_stx1_aligned.fasta > stxdir/multiassembly_stx1_aligned_clean.fasta;
+  awk '/^>/ {printf("%s%s\n",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' stxdir/multiassembly_stx1_aligned_clean.fasta > stxdir/multiassembly_stx1_aligned_linear.fasta;
+  python $tooldir/scripts/GetConsensus.py -i stxdir/multiassembly_stx1_aligned_linear.fasta -o stxdir/multiassembly_stx1_consensus.fasta;
+fi
+
+stx2filesize=$(wc -c "stxdir/multiassembly_stx2.fasta" | awk '{print $1}');
+if [ $stx2filesize -eq 0 ]
+then
+  touch stxdir/multiassembly_stx2_consensus.fasta;
+else
+  cat $tooldir/data/stx2.fa >> stxdir/multiassembly_stx2.fasta;
+  muscle -in stxdir/multiassembly_stx2.fasta -out stxdir/multiassembly_stx2_aligned.fasta;
+  awk 'BEGIN {RS=">" ; ORS=""} substr($1,1,4)!="stx2" {print ">"$0}' stxdir/multiassembly_stx2_aligned.fasta > stxdir/multiassembly_stx2_aligned_clean.fasta;
+  awk '/^>/ {printf("%s%s\n",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' stxdir/multiassembly_stx2_aligned_clean.fasta > stxdir/multiassembly_stx2_aligned_linear.fasta;
+  python $tooldir/scripts/GetConsensus.py -i stxdir/multiassembly_stx2_aligned_linear.fasta -o stxdir/multiassembly_stx2_consensus.fasta;
+fi
+cat stxdir/multiassembly_stx1_consensus.fasta > stx.fasta;
+cat stxdir/multiassembly_stx2_consensus.fasta >> stx.fasta;

test-data/blastn_H

diff -r 000000000000 -r 8be2feb96994 test-data/blastn_H

test-data/blastn_H

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_H Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,6 @@
+NODE_9_length_113741_cov_22.962397 fliC_269_AY337465_H11 99.93 1459 1 0 84783 86241 1459 1 0.0 2664 fliC_269_AY337465_H11 2913 1458 1458 0 99.93 1 1 GCAGCAGAGACAGTACGTTCTGCGTGGTCTGGTTAGCCTGCGCCAGAACAGAGGTACCCGCTTGTTGCAGGATCTGCGCACGAGACATGTTAGACACTTCGGTCGCGTAGTCAGCATCTTCGATACGGCTACGGGCAGAAGACAGGTTGTTTACGGTGTTGCCAAGGTTGGTGATAGCAGAGTCGAAACGGTTTTGTACTGCACCGAGGTCAGAACGCAGATTGTCAACTTTAGCCAATGCTTTGTCGATAGTTTCGAGCGGGTTGGTGGTAGATTGCAACGATTTTGCTGCATCTTCGTTTACCAGAATCGGGCTACCACCTTCTGATTTGCTCAGATACATGACTTTATTGTTACCAGAAGCAGTCTCCGTTATCGTTTTACCATCTGCACTAACATCGTAAGTTGCACCGTTAACAACTAACGTGCTTCCTGTTTTCTTAGCTGCATTGAGATCAAGATCGGAAAGTGTGGCAGCCTTGTTATCAACTTTGGTTGTCGTATAAAGGCCAGCGCTATTTTTGTAAACTGTCTCACTCGTAATCAAAGAAGCTTTTTTGTCAGCATCTGTCACAGTAAATGTCACTGACTTACCATCAATTTCTGCAGAATATACACCATTCCCATTGCCATCCGCTGCAGTTGTTGTTGTGAATTCAACTCCATTAAACGTGAATTTATCATTCTGTGCTTTATTCTTAGCCGCTGCTGCGAGTGCTGTAGCATCAATCCCTGTACCAGCTATGTTTGTGTCAGATTTAGTTGTCAGTGAACCATCTGCTGCACTAACAAAAATATCATTCCCTGTAGTATCTTTAACAGCTCCGCTATCTACGTTAACAGTATAAGCATCACCGCCAACATCATAGTTATCAGTACCTGTCGCTTTAAATTTAGAAATCAGGTCACTGCCAGTTGCTTTCTGCGCGCCATCGATATTAAAACCGTCCAGGCCGAGAGTTTTCGCATCAATTTTTGCCAGATTGATAGTGATGGTTTCACCATCATTAGCACCAACCTGAATTTTCATTTCATTATTTTCAGCAAGGACTTTCACGCCGTTAAACTGAGTTTGCTCAGATACACGGTCAATTTCTTCCAGACGTTGAGTAATTTCAGCCTGGATAGAAGAAAGATCGCTGTCAGAGTTAGTACCGTTAGTTGCCTGAACAGTCAGTTCACGTACACGCTGCAGGTTGTTGTTAATTTCATTCAGCGCACCTTCAGTGGTCTGCGCAACAGAAATACCATCATTCGCGTTACGGGAAGCCTGAGTCAGACCTTTAATATTTGCTGTAAAACGGTTAGCAATCGCCTGACCTGCTGCGTCATCTTTAGCACTGTTAATACGCAGGCCAGAAGAGAGACGTTCAATGGCGGAGCTCAGAGAAGACTGAGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT GCAGCAGAGACAGTACGTTCTGCGTGGTCTGGTTAGCCTGCGCCAGAACAGAGGTACCCGCTTGTTGCAGGATCTGCGCACGAGACATGTTAGACACTTCGGTCGCGTAGTCAGCATCTTCGATACGGCTACGGGCAGAAGACAGGTTGTTTACGGTGTTGCCAAGGTTGGTGATAGCAGAGTCGAAACGGTTTTGTACTGCACCGAGGTCAGAACGCAGATTGTCAACTTTAGCCAATGCTTTGTCGATAGTTTCGAGCGGGTTGGTGGTAGATTGCAACGATTTTGCTGCATCTTCGTTTACCAGAATCGGGCTACCACCTTCTGATTTGCTCAGATACATGACTTTATTGTTACCAGAAGCAGTCTCCGTTATCGTTTTACCATCTGCACTAACATCGTAAGTTGCACCGTTAACAACTAACGTGCTTCCTGTTTTCTTAGCTGCATTGAGATCAAGATCGGAAAGTGTGGCAGCCTTGTTATCAACTTTGGTTGTCGTATAAAGGCCAGCGCTATTTTTGTAAACTGTCTCACTCGTAATCAAAGAAGCTTTTTTGTCAGCATCTGTCACAGTAAATGTCACTGACTTACCATCAATTTCTGCAGAATATACACCATTCCCATTGCCATCCGCTGCAGTTGTTGTTGTGAATTCAACTCCATTAAACGTGAATTTATCATTCTGTGCTTTATTCTTAGCCGCTGCTGCGAGTGCTGTAGCATCAATCCCTGTACCAGCTATGTTTGTGTCAGATTTAGTTGTCAGTGAACCATCTGCTGCACTAACAAAAATATCATTCCCTGTAGTATCTTTAACAGCTCCGCTATCTACGTTAACAGTATAAGCATCACCGCCAACATCATAGTTATCAGTACCTGTCGCTTTAAATTTAGAAATCAGGTCACTGCCAGTTGCTTTCTGCGCGCCATCGATATTAAAACCGTCCAGGCCGAGAGTTTTCGCATCAATTTTTGCCAGATTGATAGTGATGGTTTCACCATCATTAGCACCAACCTGAATTTTCATTTCATTATTTTCAGCAAGGACTTTCACGCCGTTAAACTGAGTTTGCTCAGATACACGGTCAATTTCTTCCAGACGTTGAGTAATTTCAGCCTGGATAGAAGAAAGATCGCTGTCAGAGTTAGTACCGTTAGTTGCCTGAACAGTCAGTTCACGTACACGCTGCAGGTTGTTGTTAATTTCATTCAGCGCACCTTCAGTGGTCTGCGCAACAGAAATACCATCATTCGCGTTACGGGAAGCCTGAGTCAGACCTTTAATATTTGCTGTAAAACGGTTAGCAATCGCCTGACCTGCTGCGTCATCTTTAGCACTGTTAATACGCAGGCCAGAAGAGAGACGTTCAATGGCGGAGCTCAGAGAAGACTGAGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTGGTATTAATGACTTGTGCCAT 113741 1467 fliC_269_AY337465_H11
+NODE_9_length_113741_cov_22.962397 fliC_276_AY337472_H11 99.79 1459 3 0 84783 86241 1459 1 0.0 2655 fliC_276_AY337472_H11 2903 1456 1456 0 99.79 1 1 GCAGCAGAGACAGTACGTTCTGCGTGGTCTGGTTAGCCTGCGCCAGAACAGAGGTACCCGCTTGTTGCAGGATCTGCGCACGAGACATGTTAGACACTTCGGTCGCGTAGTCAGCATCTTCGATACGGCTACGGGCAGAAGACAGGTTGTTTACGGTGTTGCCAAGGTTGGTGATAGCAGAGTCGAAACGGTTTTGTACTGCACCGAGGTCAGAACGCAGATTGTCAACTTTAGCCAATGCTTTGTCGATAGTTTCGAGCGGGTTGGTGGTAGATTGCAACGATTTTGCTGCATCTTCGTTTACCAGAATCGGGCTACCACCTTCTGATTTGCTCAGATACATGACTTTATTGTTACCAGAAGCAGTCTCCGTTATCGTTTTACCATCTGCACTAACATCGTAAGTTGCACCGTTAACAACTAACGTGCTTCCTGTTTTCTTAGCTGCATTGAGATCAAGATCGGAAAGTGTGGCAGCCTTGTTATCAACTTTGGTTGTCGTATAAAGGCCAGCGCTATTTTTGTAAACTGTCTCACTCGTAATCAAAGAAGCTTTTTTGTCAGCATCTGTCACAGTAAATGTCACTGACTTACCATCAATTTCTGCAGAATATACACCATTCCCATT..ACCAACCTGAATTTTCATTTCATTATTTTCAGCAAGGACTTTCACGCCGTTAAACTGAGTTTGCTCAGATACACGGTCAATTTCTTCCAGACGTTGAGTAATTTCAGCCTGGATAGAAGAAAGATCGCTGTCAGAGTTAGTACCGTTAGTTGCCTGAACAGAAAGTTCACGAATACGCTGCAGGTTGTTGTTAATTTCATTCAGCGCACCTTCAGTGGTCTGCGCAACAGAAATACCATCATTCGCGTTACGGGAAGCCTGGGTCAGACCTTTAATATTTGCCGTAAAACGGTTAGCAATCGCCTGACCTGCTGCATCGTCTTTTGCGCTGTTAATACGCAGACCAGAAGACAGACGCTCAATAGCAGAGCTAAGAGAAGACTGAGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT 113741 1479 fliC_55_AJ884568_H40
+NODE_9_length_113741_cov_22.962397 fliC_84_AIHL01000060_H21 96.97 594 18 0 85648 86241 594 1 0.0 1005 fliC_84_AIHL01000060_H21 1098 576 576 0 96.97 1 1 ATAGTTATCAGTACCTGTCGCTTTAAATTTAGAAATCAGGTCACTGCCAGTTGCTTTCTGCGCGCCATCGATATTAAAACCGTCCAGGCCGAGAGTTTTCGCATCAATTTTTGCCAGATTGATAGTGATGGTTTCACCATCATTAGCACCAACCTGAATTTTCATTTCATTATTTTCAGCAAGGACTTTCACGCCGTTAAACTGAGTTTGCTCAGATACACGGTCAATTTCTTCCAGACGTTGAGTAATTTCAGCCTGGATAGAAGAAAGATCGCTGTCAGAGTTAGTACCGTTAGTTGCCTGAACAGTCAGTTCACGTACACGCTGCAGGTTGTTGTTAATTTCATTCAGCGCACCTTCAGTGGTCTGCGCAACAGAAATACCATCATTCGCGTTACGGGAAGCCTGAGTCAGACCTTTAATATTTGCTGTAAAACGGTTAGCAATCGCCTGACCTGCTGCGTCATCTTTAGCACTGTTAATACGCAGGCCAGAAGAGAGACGTTCAATGGCGGAGCTCAGAGAAGACTGAGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT ATAATTATCAGTACCTGTCGCTTTAAATTTAGAAATCAGGTCACTGCCGGTTGCTTTCTGCGCGCCATCGATATTAAAACCGTCCAGGCCGAGAGTTTTCGCATCAATTTTTGCCAGATTGATAGTGATGGTTTCACCATCATTAGCACCAACCTGAATTTTCATTTCATTATTTTCAGCAAGGACTTTCACGCCGTTAAACTGAGTTTGCTCAGATACACGGTCAATTTCTTCCAGACGTTGAGTAATTTCAGCCTGGATAGAAGAAAGATCGCTGTCAGAGTTAGTACCGTTAGTTGCCTGAACAGAAAGTTCACGAATACGCTGCAGGTTGTTGTTAATTTCATTCAGCGCACCTTCAGTGGTCTGCGCAACAGAAATACCATCATTCGCGTTACGGGAAGCCTGGGTCAGACCTTTAATATTTGCCGTAAAACGGTTAGCAATCGCCTGACCTGCTGCATCGTCTTTTGCGCTGTTAATACGCAGACCAGAAGACAGACGCTCAATAGCAGAGCTAAGAGAAGACTGAGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT 113741 1476 fliC_84_AIHL01000060_H21
+NODE_9_length_113741_cov_22.962397 fliC_84_AIHL01000060_H21 95.67 531 23 0 84778 85308 1476 946 0.0 867 fliC_84_AIHL01000060_H21 947 508 508 0 95.67 1 1 TTAACGCAGCAGAGACAGTACGTTCTGCGTGGTCTGGTTAGCCTGCGCCAGAACAGAGGTACCCGCTTGTTGCAGGATCTGCGCACGAGACATGTTAGACACTTCGGTCGCGTAGTCAGCATCTTCGATACGGCTACGGGCAGAAGACAGGTTGTTTACGGTGTTGCCAAGGTTGGTGATAGCAGAGTCGAAACGGTTTTGTACTGCACCGAGGTCAGAACGCAGATTGTCAACTTTAGCCAATGCTTTGTCGATAGTTTCGAGCGGGTTGGTGGTAGATTGCAACGATTTTGCTGCATCTTCGTTTACCAGAATCGGGCTACCACCTTCTGATTTGCTCAGATACATGACTTTATTGTTACCAGAAGCAGTCTCCGTTATCGTTTTACCATCTGCACTAACATCGTAAGTTGCACCGTTAACAACTAACGTGCTTCCTGTTTTCTTAGCTGCATTGAGATCAAGATCGGAAAGTGTGGCAGCCTTGTTATCAACTTTGGTTGTCGTATAAAGGCCAGCGCTATTTTTGTA TTAACGCAGCAGAGACAGTACGTTCTGCGTGGTCTGGTTAGCCTGTGCCAGAACAGAGGTACCCGCTTGTTGCAGGATCTGCGCACGAGACATGTTAGACACTTCGGTCGCGTAGTCAGCATCTTCGATACGGCTACGGGCAGAAGACAGGTTGTTTACGGTGTTGCCAAGGTTGGTGATGGCAGAGTCGAAACGGTTTTGTACTGCACCGAGGTCAGAACGCAGATTGTCAACTTTAGCCAATGCTTTGTCGATAGTTTCGAGCGGGTTGGTGGTAGATTGCAACGATTTTGCTGCATCTTCGTTTACCAGAATCGGGCTACCACCTTCTGATTTGCTCAGATACATGACTTTATTGTTACCAGAAGCAGTCTCCGTTATCGTTTTACCATCTGCACTAACATCGTAAGTTGCACCGTTAACAACTAACGTGCTTCCTGTTTTCTTGGCAGCGTTCAGATCAAGATCAGATAGTGTCGCTGCTTTATTTTCAACTTTTGTTGCAGTCAATTGCCCTGCACTATTTTTGTA 113741 1476 fliC_84_AIHL01000060_H21
+NODE_9_length_113741_cov_22.962397 fliC_109_AM231154_H27 98.56 348 5 0 84778 85125 1461 1114 2e-175 614 fliC_109_AM231154_H27 671 343 343 0 98.56 1 1 TTAACGCAGCAGAGACAGTACGTTCTGCGTGGTCTGGTTAGCCTGCGCCAGAACAGAGGTACCCGCTTGTTGCAGGATCTGCGCACGAGACATGTTAGACACTTCGGTCGCGTAGTCAGCATCTTCGATACGGCTACGGGCAGAAGACAGGTTGTTTACGGTGTTGCCAAGGTTGGTGATAGCAGAGTCGAAACGGTTTTGTACTGCACCGAGGTCAGAACGCAGATTGTCAACTTTAGCCAATGCTTTGTCGATAGTTTCGAGCGGGTTGGTGGTAGATTGCAACGATTTTGCTGCATCTTCGTTTACCAGAATCGGGCTACCACCTTCTGATTTGCTCAGATACAT TTACCGCAGCAGAGACAGTACGTTCTGCGTGGTCTGGTTAGCCTGCGCCAGAACAGAGGTACCCGCTTGTTGCAGGATCTGCGCACGAGACATGTTAGACACTTCGGTCGCGTAGTCAGCATCTTCGATACGGCTACGGGCAGAAGACAGGTTGTTTACGGTGTTGCCAAGGTTGGTGATAGCAGAGTCGAAACGGTTTTGTACTGCACCGAGGTCAGAACGCAGATTGTCAACTTTAGCCAATGCCTTGTCGATGGTTTCGAGCGGGTTGGTAGTAGATTGCAACGATTTTGCTGCATCTTCTTTTACCAGAATCGGGCTACCACCTTCTGATTTGCTCAGATACAT 113741 1461 fliC_109_AM231154_H27

test-data/blastn_O

diff -r 000000000000 -r 8be2feb96994 test-data/blastn_O

test-data/blastn_O

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_O Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,5 @@
+NODE_4_length_135594_cov_24.959756 wzx_208_AF529080_O26 100.00 1263 0 0 32907 34169 1263 1 0.0 2278 wzx_208_AF529080_O26 2526 1263 1263 0 100.00 1 1 TTATAATCGTTTCACTTTATAAATTCTAAGTATGAGAATAAGTAAGATAAACTCAGCAAATACATAAGCAATTGCAGCGCCTATTTCAGCAAAGAAATAACTCAGGCATAATGATAAAATAATAGTTGAAACACCCGTAATGGCCACTATATAAGAAAATTCTTTTTTATACCCTCTTATGGACAATCCAACCGAACCAAACATAAAATTGTATATCCCCATAAATATTGCAAAAGACATTATTGATAAAGGGATGAACGCGCTTCTAATTTCAGCGATACTTTGAACCTTATATCCCAATATAGTACCCACCCCCCCTAAACTCAGGACAATGAAAACCATGAACTTTAGCTGAATATTTGTGCTTGCATATAGCAGGCTTTTATATTCTCCAACTTTGTATGGTTCTAATTTCAATTCATGTTGCTTTATCAACCTCGTGAAATAGTATTGATTTAACGGGGTTGCTATAGACTGAATACATTTAATAATTTTCTCTGCCGTCGCGTACAGAGACGTTGCAACAGGCGAAGCAAGAGTGCCAAGAATAATAATATTACTATTTCTGTATAGAATAACAAATATATTAGCAATAAACAGATGATAACCTGTGCATATATATTCTAAAATTTCCGCCCATTGAATTTTAGCTTTATTAGTCTTATTTTGATAATATATATATATAAGCGATAGCACGCCAGATAAAAAATACGAACCAGACACACAAATGACATAATAATAACTTGTTAAATAGCCTGCTGGTCCATTATAAAAATAAATAAGACATAATGACATACCACGAGCAATTAGTACAAAAACAGCCAATGGCCTATTGTTATTCGTAGCCTGAAAAAAATAATTAGATTGCAATATCATCCCTACTGGGTACAATAAAAACAATCCCAAGTATACACTTAATGTTTTATTAATTAAATACGTTATAAATAAAAGACATATTCCTGAAATAACAAATAAACACAACCTACAGATTAGTGTCAGAATGTAAACTTTAAATATTTCATCTTTTGTCACACTTGAAATTACCTTCTGCACACTTATAATATCAAAACTGTATAGCGAAAATATAAGCACATATAGTGCTAGTACTTCACCAACAGCAATACTTGAAAAGATGTTTTCCCCTAAGGTAATAAGAAAAAATGGGAATACCAACACAGGAAATATGGCATTCGCACCCTGAATTATTGCCAACTCCAATACTGAATGATATTCCTTTATTTTTTGAAGTTTTTTTTTCAACAT TTATAATCGTTTCACTTTATAAATTCTAAGTATGAGAATAAGTAAGATAAACTCAGCAAATACATAAGCAATTGCAGCGCCTATTTCAGCAAAGAAATAACTCAGGCATAATGATAAAATAATAGTTGAAACACCCGTAATGGCCACTATATAAGAAAATTCTTTTTTATACCCTCTTATGGACAATCCAACCGAACCAAACATAAAATTGTATATCCCCATAAATATTGCAAAAGACATTATTGATAAAGGGATGAACGCGCTTCTAATTTCAGCGATACTTTGAACCTTATATCCCAATATAGTACCCACCCCCCCTAAACTCAGGACAATGAAAACCATGAACTTTAGCTGAATATTTGTGCTTGCATATAGCAGGCTTTTATATTCTCCAACTTTGTATGGTTCTAATTTCAATTCATGTTGCTTTATCAACCTCGTGAAATAGTATTGATTTAACGGGGTTGCTATAGACTGAATACATTTAATAATTTTCTCTGCCGTCGCGTACAGAGACGTTGCAACAGGCGAAGCAAGAGTGCCAAGAATAATAATATTACTATTTCTGTATAGAATAACAAATATATTAGCAATAAACAGATGATAACCTGTGCATATATATTCTAAAATTTCCGCCCATTGAATTTTAGCTTTATTAGTCTTATTTTGATAATATATATATATAAGCGATAGCACGCCAGATAAAAAATACGAACCAGACACACAAATGACATAATAATAACTTGTTAAATAGCCTGCTGGTCCATTATAAAAATAAATAAGACATAATGACATACCACGAGCAATTAGTACAAAAACAGCCAATGGCCTATTGTTATTCGTAGCCTGAAAAAAATAATTAGATTGCAATATCATCCCTACTGGGTACAATAAAAACAATCCCAAGTATACACTTAATGTTTTATTAATTAAATACGTTATAAATAAAAGACATATTCCTGAAATAACAAATAAACACAACCTACAGATTAGTGTCAGAATGTAAACTTTAAATATTTCATCTTTTGTCACACTTGAAATTACCTTCTGCACACTTATAATATCAAAACTGTATAGCGAAAATATAAGCACATATAGTGCTAGTACTTCACCAACAGCAATACTTGAAAAGATGTTTTCCCCTAAGGTAATAAGAAAAAATGGGAATACCAACACAGGAAATATGGCATTCGCACCCTGAATTATTGCCAACTCCAATACTGAATGATATTCCTTTATTTTTTGAAGTTTTTTTTTCAACAT 135594 1263 wzx_208_AF529080_O26
+NODE_4_length_135594_cov_24.959756 wzy_192_AF529080_O26 100.00 1023 0 0 31819 32841 1023 1 0.0 1846 wzy_192_AF529080_O26 2046 1023 1023 0 100.00 1 1 TCATAATGAGTATGGTAACCCAAATACAATGTAATCATAATCGATTTGGAGTGTATAATATATTGATAATGCAAAAGTGAATAACAGTAAATATGAATAAAGTATATATCTGGTCGGTCTACTTAAATACTGTGCGATAGACATCATTACCAGATACTTCAGTAATAGCGCATTTCGAAAAATCCTATTTATTTCGTCGATATATAAAAGTAGTGGTGAAAATACGGAAAGAAATAACATTAGCGAGAATATTATATCAATCCATTGTTTAGTATGTAAATCAGTTATTACTATTTTTTTTCTGAAGTAACATAACAGAAAAAGATCAAAAAGATAAGGACCTGCCCATATAATAAGAGAATGAACCTTAATGCCATCAGCTATATATGCATGTAACGTCCTAGTGTTAAATAATAAAATTAACATTTTAATCAAGAGTGGCACTACAATAAAAGACAGCACCAGTCCAAAAACCATTAACTTATTATAACCCCTCCAGGTACGAAATTGGATTATTACCCACGCCAATACATAAACAATGCCTAAACTATGGAAAAGAGGTGCCATAAAGACAAAACAAAGAGAGTTAAATTTATGCTCTTTTTCTAACTCGATAAGAGAATTTATGACAAATAAAAAAAGAAATGTATTCCTGATTTGAACAATGTCAATAGGCATTGGACACAACATGTAAAGCAGCAAACCAAATGCTGTATACTTACTGTATTGTATTAATCGTAGGAATGTGGTCCCAAGGAATAAACCCAGCAAGCCAATTATGACTTCATGGGTACCGCCTAAATACTTAACACCATAAATTAACCAGCGATAACCAATCTCGGCATAAAGTTCATTGACATTAAATATATCAACATACGCTTCATAGTCTTGATTCTGCCTATTAATAATAAATAAAGTAGTAATAATAAGCACAATTACCAAATTACTTAGCTTGTTTGCTCTAGCGTAGTTGAATGCAATAATCCATAAACCTAAAACCATCACAAATATGATGTAATACAT TCATAATGAGTATGGTAACCCAAATACAATGTAATCATAATCGATTTGGAGTGTATAATATATTGATAATGCAAAAGTGAATAACAGTAAATATGAATAAAGTATATATCTGGTCGGTCTACTTAAATACTGTGCGATAGACATCATTACCAGATACTTCAGTAATAGCGCATTTCGAAAAATCCTATTTATTTCGTCGATATATAAAAGTAGTGGTGAAAATACGGAAAGAAATAACATTAGCGAGAATATTATATCAATCCATTGTTTAGTATGTAAATCAGTTATTACTATTTTTTTTCTGAAGTAACATAACAGAAAAAGATCAAAAAGATAAGGACCTGCCCATATAATAAGAGAATGAACCTTAATGCCATCAGCTATATATGCATGTAACGTCCTAGTGTTAAATAATAAAATTAACATTTTAATCAAGAGTGGCACTACAATAAAAGACAGCACCAGTCCAAAAACCATTAACTTATTATAACCCCTCCAGGTACGAAATTGGATTATTACCCACGCCAATACATAAACAATGCCTAAACTATGGAAAAGAGGTGCCATAAAGACAAAACAAAGAGAGTTAAATTTATGCTCTTTTTCTAACTCGATAAGAGAATTTATGACAAATAAAAAAAGAAATGTATTCCTGATTTGAACAATGTCAATAGGCATTGGACACAACATGTAAAGCAGCAAACCAAATGCTGTATACTTACTGTATTGTATTAATCGTAGGAATGTGGTCCCAAGGAATAAACCCAGCAAGCCAATTATGACTTCATGGGTACCGCCTAAATACTTAACACCATAAATTAACCAGCGATAACCAATCTCGGCATAAAGTTCATTGACATTAAATATATCAACATACGCTTCATAGTCTTGATTCTGCCTATTAATAATAAATAAAGTAGTAATAATAAGCACAATTACCAAATTACTTAGCTTGTTTGCTCTAGCGTAGTTGAATGCAATAATCCATAAACCTAAAACCATCACAAATATGATGTAATACAT 135594 1023 wzy_192_AF529080_O26
+NODE_4_length_135594_cov_24.959756 wzx_144_AB812060_O140 95.56 45 2 0 37707 37751 45 1 6e-12 73.4 wzx_144_AB812060_O140 80 43 43 0 95.56 1 1 ATGCACGCTACCGCCCCTGGCTTTACAGCTACCAGTGCACTGCAT ATCCACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCAT 135594 1314 wzx_144_AB812060_O140
+NODE_4_length_135594_cov_24.959756 wzx_164_EU294176_O159 97.62 42 1 0 37710 37751 42 1 2e-11 71.6 wzx_164_EU294176_O159 78 41 41 0 97.62 1 1 CACGCTACCGCCCCTGGCTTTACAGCTACCAGTGCACTGCAT CACGCTACCGCCCCTGGCTTTACAGCTACCAGAGCACTGCAT 135594 1380 wzx_164_EU294176_O159
+NODE_57_length_30709_cov_37.569322 wzy_222_AB812027_O68 100.00 28 0 0 21814 21841 1080 1107 4e-06 51.8 wzy_222_AB812027_O68 56 28 28 0 100.00 1 1 GGAAGGTGCGAACAAGTTCCTGATATGA GGAAGGTGCGAACAAGTTCCTGATATGA 30709 1107 wzy_222_AB812027_O68

test-data/report_out.html

diff -r 000000000000 -r 8be2feb96994 test-data/report_out.html

test-data/report_out.html

--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report_out.html Fri Mar 11 15:50:35 2022 -0500
@@ -0,0 +1,160 @@
+<!DOCTYPE html><html><head><title>EURL VTEC Typer summary report</title>
+  <style type="text/css">
+    body {font-family:"sans-serif","lucida Sans Unicode","Lucida Grande","Segoe UI";font-size:13px;}
+    h1 {font-weight:normal;font-size:2em;margin-top:0.3em;margin-bottom:0.3em;}
+    h4 {font-size:1.17em;margin-top:0;margin-bottom:0;}
+    .table-head td {border:1px solid #73ad21;border-radius:6px;}
+    .table-rep {border-collapse:collapse;font-size:13px;margin:auto;}
+    .table-rep th, .table-rep td {padding:5px 5px;}
+    .table-rep .title {caption-side:top;margin-top:12px;margin-bottom:6px;font-size:24px;text-align:left;}
+    .table-rep tbody td:last-child {border:0;}
+    .table-rep thead th:last-child {border:0; border-bottom: 1px solid #d7e1da;}
+    .table-rep thead th {border-right:1px solid #d7e1da;border-bottom:1px solid #d7e1da;}
+    .table-rep tbody td {color:#353535;border-right:1px solid #d7e1da;text-align:right;}
+    .table-rep tbody tr:nth-child(odd) td {background-color:#f4fff7;}
+    .table-rep tbody tr:nth-child(even) td {background-color:#e2e2e2;}
+    .table-cross tbody td {color:#353535;border-right:1px solid #d7e1da;text-align:right;}
+    .table-cross {border-collapse:collapse;font-size:13px;margin:auto;}
+    .table-cross th, .table-cross td {max-width:220px; word-wrap:break-word;}
+    .table-cross tr:nth-child(2n+1) {background: rgba(178, 178, 178, 0.5) none repeat scroll 0 0;}
+    .table-cross th:nth-child(2n), .table-cross td:nth-child(2n) {background: rgba(178, 178, 178, 0.5) none repeat scroll 0 0;}
+  </style> <meta charset='utf-8'>
+<body><div style="border: 1px solid #73ad21;max-width:940px;text-align:center;margin:auto;"></br>
+<table class="table table-head"><tr><td width="25%"><img src='https://aries.iss.it/static/images/aries.jpg' alt='ARIES' style='float:left;width:50%;padding-left:0.5cm;'>
+<img src='https://aries.iss.it/static/images/isseurlvtec.png' alt='ISS-EURL VTEC' style='float:left;width:30%'></td>
+<td><h1>EURL VTEC Typer</h1><h2>Report for Strain_1_L2.fastq</h2>2018-05-17 11:16 UTC</td><td style='width: 25%; padding-left: 0.2cm; text-align: left;'><h4>Istituto Superiore di Sanità</h4>
+Department of Food Safety, Nutrition and Veterinary Public Health<br/>European Union Reference Laboratory for <i>E. coli</i></td></tr></table>
+<h3>Summary</h3>
+O26:H11<br/>ST21<br/><p>eae, ehxa, stx1a, stx1b
+</p>
+<br/><hr/><h3>Raw data quality check</h3>
+<p>FASTQC result: <a href='https://galaxy.iss.it/datasets/4b25789cdf945d7e/display/?preview=True'>Webpage</a></p>
+<br/><hr/><h3>Trimming analysis</h3>
+<table cellpadding="4" class="table table-rep">
+<tr><td>Maximum length trimming</td><td>360</td></tr>
+<tr><td>Left-side trimming</td><td>10</td></tr>
+<tr><td>Right-side trimming</td><td>0</td></tr>
+<tr><td>Minimum Phred quality score for right-side trimming</td><td>25</td></tr>
+<tr><td>Average Phred quality score for right-side trimming</td><td>27</td></tr>
+<tr><td>Minimum length filtering</td><td>50</td></tr>
+</table><br/><hr/><h3>Assembly statistics</h3>
+<table cellpadding="4" class="table table-rep">
+<tr><td>Estimated genome size:</td><td>5000000 bp
+</td></tr>
+<tr><td>Assembled nucleotides:</td><td>5493390 bp
+</td></tr>
+<tr><td>Estimated coverage:</td><td>1.1 x
+</td></tr>
+<tr><td>N. contigs:</td><td>315
+</td></tr>
+<tr><td>Average contig length:</td><td>17439
+</td></tr>
+<tr><td>Median contig length:</td><td>4504
+</td></tr>
+<tr><td>Maximum contig length:</td><td>164788
+</td></tr>
+<tr><td>N. contigs >= 200 bp:</td><td>315 (100.0 %)
+</td></tr>
+<tr><td>N. contigs >= 2,000 bp:</td><td>224 (71.1 %)
+</td></tr>
+<tr><td>N50:</td><td>52450
+</td></tr>
+<tr><td>NG50:</td><td>59152
+</td></tr>
+</table><br/><hr/><h3>Serotyping</h3>
+<table cellpadding="4" class="table table-rep">
+<tr><th>sseqid</th><th>pident</th><th>length</th><th>positiv..3_af054421</a></td><td>93.12</td><td>10.91</td><td>99.89
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab456530'>toxb_3_ab456530</a></td><td>100.0</td><td>27.15</td><td>99.98
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/am230663'>stx1b_14_am230663_a</a></td><td>100.0</td><td>18.51</td><td>100.0
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/x06119'>celb_9_x06119</a></td><td>100.0</td><td>177.13</td><td>99.31
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010953'>iha_5_ap010953</a></td><td>100.0</td><td>38.17</td><td>100.0
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/gq259888'>espp_3_gq259888</a></td><td>100.0</td><td>41.34</td><td>100.0
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af461168'>stx1a_15_af461168_a</a></td><td>99.89</td><td>20.92</td><td>99.79
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/aj225018'>espa_23_aj225018</a></td><td>100.0</td><td>9.57</td><td>100.0
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010960'>nlec_6_ap010960</a></td><td>100.0</td><td>18.57</td><td>99.8
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010953'>lpfa_3_ap010953</a></td><td>100.0</td><td>15.77</td><td>100.0
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af453441'>nleb_11_af453441</a></td><td>97.58</td><td>12.94</td><td>99.9
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fj386569'>toxb_4_fj386569</a></td><td>100.0</td><td>25.5</td><td>99.97
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ae014075'>iss_11_ae014075</a></td><td>100.0</td><td>15.83</td><td>97.66
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/x94129'>ehxa_4_x94129</a></td><td>93.56</td><td>16.28</td><td>99.71
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fm201463'>espa_22_fm201463</a></td><td>100.0</td><td>18.99</td><td>100.0
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/am422003'>nlea_12_am422003</a></td><td>100.0</td><td>21.17</td><td>100.0
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab071620'>stx1b_11_ab071620_c</a></td><td>100.0</td><td>11.84</td><td>99.63
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ecu59503'>eae_45_ecu59503</a></td><td>92.62</td><td>28.63</td><td>99.85
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab011549'>espp_4_ab011549</a></td><td>95.62</td><td>29.83</td><td>99.87
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/hm138194'>espp_1_hm138194</a></td><td>99.03</td><td>37.41</td><td>99.97
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ay128535'>cif_2_ay128535</a></td><td>99.88</td><td>19.24</td><td>99.88
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ay128537'>cif_1_ay128537</a></td><td>99.88</td><td>18.14</td><td>99.88
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab303060'>espj_1_ab303060</a></td><td>100.0</td><td>63.45</td><td>100.0
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fm201463'>nleb_12_fm201463</a></td><td>93.54</td><td>16.32</td><td>99.57
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010953'>nlec_3_ap010953</a></td><td>94.53</td><td>20.93</td><td>99.46
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fj386569'>ehxa_5_fj386569</a></td><td>99.63</td><td>23.12</td><td>99.97
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/cu928158'>iss_12_cu928158</a></td><td>100.0</td><td>23.77</td><td>99.42
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/d00021'>celb_10_d00021</a></td><td>100.0</td><td>150.01</td><td>98.61
+</td></tr>
+<tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/gq259888'>toxb_2_gq259888</a></td><td>99.29</td><td>24.57</td><td>99.98
+</td></tr>
+</table><br/></div></body></html>
+