--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SalmID/SalmID.py	Fri Nov 09 11:30:45 2018 -0500
@@ -0,0 +1,371 @@
+#!/usr/bin/env python3
+
+
+import gzip
+import io
+import pickle
+import os
+import sys
+
+from argparse import ArgumentParser
+try:
+	from version import SalmID_version
+except:
+    SalmID_version = "version unknown"
+
+
+def reverse_complement(sequence):
+    complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N', 'M': 'K', 'R': 'Y', 'W': 'W',
+                            'S': 'S', 'Y': 'R', 'K': 'M', 'V': 'B', 'H': 'D', 'D': 'H', 'B': 'V'}
+    return "".join(complement[base] for base in reversed(sequence))
+
+
+def parse_args():
+    "Parse the input arguments, use '-h' for help."
+    parser = ArgumentParser(description='SalmID - rapid Kmer based Salmonella identifier from sequence data')
+    # inputs
+    parser.add_argument('-v','--version', action='version', version='%(prog)s ' + SalmID_version)
+    parser.add_argument(
+        '-i','--input_file', type=str, required=False, default= 'None', metavar = 'your_fastqgz',
+        help='Single fastq.gz file input, include path to file if file is not in same directory ')
+    parser.add_argument(
+        '-e', '--extension', type=str, required=False, default= '.fastq.gz', metavar = 'file_extension',
+        help='File extension, if specified without "--input_dir", SalmID will attempt to ID all files\n' +
+             ' with this extension in current directory, otherwise files in input directory')
+
+    parser.add_argument(
+        '-d','--input_dir', type=str, required=False, default='.', metavar = 'directory',
+        help='Directory which contains data for identification, when not specified files in current directory will be analyzed.')
+    parser.add_argument(
+        '-r', '--report', type=str, required=False, default='percentage', metavar = 'percentage, coverage or taxonomy',
+        help='Report either percentage ("percentage") of clade specific kmers recovered, average kmer-coverage ("cov"), or '
+             'taxonomy (taxonomic species ID, plus observed mean k-mer coverages and expected coverage).')
+    parser.add_argument(
+        '-m', '--mode', type=str, required=False, default='quick', metavar = 'quick or thorough',
+        help='Quick [quick] or thorough [thorough] mode')
+    if len(sys.argv)==1:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
+    return parser.parse_args()
+
+def get_av_read_length(file):
+    i = 1
+    n_reads = 0
+    total_length = 0
+    if file.endswith(".gz"):
+        file_content=io.BufferedReader(gzip.open(file))
+    else:
+        file_content=open(file,"r").readlines()
+    for line in file_content:
+        if i % 4 == 2:
+            total_length += len(line.strip())
+            n_reads +=1
+        i += 1
+        if n_reads == 100:
+            break
+    return total_length/100
+
+
+def createKmerDict_reads(list_of_strings, kmer):
+    kmer_table = {}
+    for string in list_of_strings:
+        sequence = string.strip('\n')
+        for i in range(len(sequence)-kmer+1):
+            new_mer =sequence[i:i+kmer]
+            new_mer_rc = reverse_complement(new_mer)
+            if new_mer in kmer_table:
+                kmer_table[new_mer.upper()] += 1
+            else:
+                kmer_table[new_mer.upper()] = 1
+            if new_mer_rc in kmer_table:
+                kmer_table[new_mer_rc.upper()] += 1
+            else:
+                kmer_table[new_mer_rc.upper()] = 1
+    return kmer_table
+
+
+def target_read_kmerizer_multi(file, k, kmerDict_1, kmerDict_2, mode):
+    mean_1 = None
+    mean_2 = None
+    i = 1
+    n_reads_1 = 0
+    n_reads_2 = 0
+    total_coverage_1 = 0
+    total_coverage_2 = 0
+    reads_1 = []
+    reads_2 = []
+    total_reads = 0
+    if file.endswith(".gz"):
+      file_content=io.BufferedReader(gzip.open(file))
+    else:
+      file_content=open(file,"r").readlines()
+    for line in file_content:
+        start = int((len(line) - k) // 2)
+        if i % 4 == 2:
+            total_reads += 1
+            if file.endswith(".gz"):
+                s1 = line[start:k + start].decode()
+                line=line.decode()
+            else:
+                s1 = line[start:k + start]
+            if s1 in kmerDict_1:
+                n_reads_1 += 1
+                total_coverage_1 += len(line)
+                reads_1.append(line)
+            if s1 in kmerDict_2:
+                n_reads_2 += 1
+                total_coverage_2 += len(line)
+                reads_2.append(line)
+        i += 1
+        if mode == 'quick':
+            if total_coverage_2 >= 800000:
+                break
+
+    if len(reads_1) == 0:
+        kmer_Dict1 = {}
+    else:
+        kmer_Dict1 = createKmerDict_reads(reads_1, k)
+        mers_1 = set([key for key in kmer_Dict1])
+        mean_1 = sum([kmer_Dict1[key] for key in kmer_Dict1])/len(mers_1)
+    if len(reads_2) == 0:
+        kmer_Dict2 = {}
+    else:
+        kmer_Dict2 = createKmerDict_reads(reads_2, k)
+        mers_2 = set([key for key in kmer_Dict2])
+        mean_2 = sum([kmer_Dict2[key] for key in kmer_Dict2])/len(mers_2)
+    return kmer_Dict1, kmer_Dict2, mean_1, mean_2, total_reads
+
+def mean_cov_selected_kmers(iterable, kmer_dict, clade_specific_kmers):
+    '''
+    Given an iterable (list, set, dictrionary) returns mean coverage for the kmers in iterable
+    :param iterable: set, list or dictionary containing kmers
+    :param kmer_dict: dictionary with kmers as keys, kmer-frequency as value
+    :param  clade_specific_kmers: list, dict or set of clade specific kmers
+    :return: mean frequency as float
+    '''
+    if len(iterable) == 0:
+        return 0
+    return sum([kmer_dict[value] for value in iterable])/len(clade_specific_kmers)
+
+def kmer_lists(query_fastq_gz, k,
+               allmers,allmers_rpoB,
+               uniqmers_bongori,
+               uniqmers_I,
+               uniqmers_IIa,
+               uniqmers_IIb,
+               uniqmers_IIIa,
+               uniqmers_IIIb,
+               uniqmers_IV,
+               uniqmers_VI,
+               uniqmers_VII,
+               uniqmers_VIII,
+               uniqmers_bongori_rpoB,
+               uniqmers_S_enterica_rpoB,
+               uniqmers_Escherichia_rpoB,
+               uniqmers_Listeria_ss_rpoB,
+               uniqmers_Lmono_rpoB,
+               mode):
+    dict_invA, dict_rpoB, mean_invA, mean_rpoB , total_reads = target_read_kmerizer_multi(query_fastq_gz, k, allmers,
+                                                                            allmers_rpoB, mode)
+    target_mers_invA = set([key for key in dict_invA])
+    target_mers_rpoB = set([key for key in dict_rpoB])
+    if target_mers_invA == 0:
+        print('No reads found matching invA, no Salmonella in sample?')
+    else:
+        p_bongori = (len(uniqmers_bongori & target_mers_invA) / len(uniqmers_bongori)) * 100
+        p_I = (len(uniqmers_I & target_mers_invA) / len(uniqmers_I)) * 100
+        p_IIa = (len(uniqmers_IIa & target_mers_invA) / len(uniqmers_IIa)) * 100
+        p_IIb = (len(uniqmers_IIb & target_mers_invA) / len(uniqmers_IIb)) * 100
+        p_IIIa = (len(uniqmers_IIIa & target_mers_invA) / len(uniqmers_IIIa)) * 100
+        p_IIIb = (len(uniqmers_IIIb & target_mers_invA) / len(uniqmers_IIIb)) * 100
+        p_VI = (len(uniqmers_VI & target_mers_invA) / len(uniqmers_VI)) * 100
+        p_IV = (len(uniqmers_IV & target_mers_invA) / len(uniqmers_IV)) * 100
+        p_VII = (len(uniqmers_VII & target_mers_invA) / len(uniqmers_VII)) * 100
+        p_VIII = (len(uniqmers_VIII & target_mers_invA) / len(uniqmers_VIII)) * 100
+        p_bongori_rpoB = (len(uniqmers_bongori_rpoB & target_mers_rpoB) / len(uniqmers_bongori_rpoB)) * 100
+        p_Senterica = (len(uniqmers_S_enterica_rpoB & target_mers_rpoB) / len(uniqmers_S_enterica_rpoB)) * 100
+        p_Escherichia = (len(uniqmers_Escherichia_rpoB & target_mers_rpoB) / len(uniqmers_Escherichia_rpoB)) * 100
+        p_Listeria_ss = (len(uniqmers_Listeria_ss_rpoB & target_mers_rpoB) / len(uniqmers_Listeria_ss_rpoB)) * 100
+        p_Lmono = (len(uniqmers_Lmono_rpoB & target_mers_rpoB) / len(uniqmers_Lmono_rpoB)) * 100
+        bongori_invA_cov = mean_cov_selected_kmers(uniqmers_bongori & target_mers_invA, dict_invA, uniqmers_bongori)
+        I_invA_cov = mean_cov_selected_kmers(uniqmers_I & target_mers_invA, dict_invA, uniqmers_I)
+        IIa_invA_cov = mean_cov_selected_kmers(uniqmers_IIa & target_mers_invA, dict_invA, uniqmers_IIa)
+        IIb_invA_cov = mean_cov_selected_kmers(uniqmers_IIb & target_mers_invA, dict_invA, uniqmers_IIb)
+        IIIa_invA_cov = mean_cov_selected_kmers(uniqmers_IIIa & target_mers_invA, dict_invA, uniqmers_IIIa)
+        IIIb_invA_cov = mean_cov_selected_kmers(uniqmers_IIIb & target_mers_invA, dict_invA, uniqmers_IIIb)
+        IV_invA_cov = mean_cov_selected_kmers(uniqmers_IV & target_mers_invA, dict_invA, uniqmers_IV)
+        VI_invA_cov = mean_cov_selected_kmers(uniqmers_VI & target_mers_invA, dict_invA, uniqmers_VI)
+        VII_invA_cov = mean_cov_selected_kmers(uniqmers_VII & target_mers_invA, dict_invA, uniqmers_VII)
+        VIII_invA_cov = mean_cov_selected_kmers(uniqmers_VIII & target_mers_invA, dict_invA, uniqmers_VIII)
+        S_enterica_rpoB_cov = mean_cov_selected_kmers((uniqmers_S_enterica_rpoB & target_mers_rpoB), dict_rpoB,
+                                                      uniqmers_S_enterica_rpoB)
+        S_bongori_rpoB_cov = mean_cov_selected_kmers((uniqmers_bongori_rpoB & target_mers_rpoB), dict_rpoB,
+                                                     uniqmers_bongori_rpoB)
+        Escherichia_rpoB_cov = mean_cov_selected_kmers((uniqmers_Escherichia_rpoB & target_mers_rpoB), dict_rpoB,
+                                                       uniqmers_Escherichia_rpoB)
+        Listeria_ss_rpoB_cov = mean_cov_selected_kmers((uniqmers_Listeria_ss_rpoB & target_mers_rpoB), dict_rpoB,
+                                                       uniqmers_Listeria_ss_rpoB)
+        Lmono_rpoB_cov = mean_cov_selected_kmers((uniqmers_Lmono_rpoB & target_mers_rpoB), dict_rpoB,
+                                                 uniqmers_Lmono_rpoB)
+        coverages = [Listeria_ss_rpoB_cov, Lmono_rpoB_cov, Escherichia_rpoB_cov, S_bongori_rpoB_cov,
+                     S_enterica_rpoB_cov, bongori_invA_cov, I_invA_cov, IIa_invA_cov, IIb_invA_cov,
+                     IIIa_invA_cov, IIIb_invA_cov, IV_invA_cov, VI_invA_cov, VII_invA_cov, VIII_invA_cov]
+        locus_scores = [p_Listeria_ss, p_Lmono, p_Escherichia, p_bongori_rpoB, p_Senterica, p_bongori,
+                        p_I, p_IIa,p_IIb, p_IIIa, p_IIIb, p_IV, p_VI, p_VII, p_VIII]
+    return locus_scores, coverages, total_reads
+
+def report_taxon(locus_covs, average_read_length, number_of_reads):
+    list_taxa = [ 'Listeria ss', 'Listeria monocytogenes', 'Escherichia sp.',
+                  'Salmonella bongori (rpoB)', 'Salmonella enterica (rpoB)',
+                  'Salmonella bongori (invA)', 'S. enterica subsp. enterica (invA)',
+                  'S. enterica subsp. salamae (invA: clade a)','S. enterica subsp. salamae (invA: clade b)',
+                  'S. enterica subsp. arizonae (invA)', 'S. enterica subsp. diarizonae (invA)',
+                  'S. enterica subsp. houtenae (invA)', 'S. enterica subsp. indica (invA)',
+                  'S. enterica subsp. VII (invA)', 'S. enterica subsp. salamae (invA: clade VIII)']
+    if sum(locus_covs) < 1:
+        rpoB = ('No rpoB matches!', 0)
+        invA = ('No invA matches!', 0)
+        return rpoB, invA, 0.0
+    else:
+        # given list of scores get taxon
+        if sum(locus_covs[0:5]) > 0:
+            best_rpoB = max(range(len(locus_covs[1:5])), key=lambda x: locus_covs[1:5][x])+1
+            all_rpoB = max(range(len(locus_covs[0:5])), key=lambda x: locus_covs[0:5][x])
+            if (locus_covs[best_rpoB] != 0) & (all_rpoB == 0):
+                rpoB = (list_taxa[best_rpoB], locus_covs[best_rpoB])
+            elif (all_rpoB == 0) &  (round(sum(locus_covs[1:5]),1) < 1):
+                rpoB = (list_taxa[0], locus_covs[0])
+            else:
+                rpoB = (list_taxa[best_rpoB], locus_covs[best_rpoB])
+        else:
+            rpoB = ('No rpoB matches!', 0)
+        if sum(locus_covs[5:]) > 0:
+            best_invA = max(range(len(locus_covs[5:])), key=lambda x: locus_covs[5:][x])+5
+            invA = (list_taxa[best_invA], locus_covs[best_invA])
+        else:
+            invA = ('No invA matches!', 0)
+        if 'Listeria' in rpoB[0]:
+            return rpoB, invA, (average_read_length * number_of_reads) / 3000000
+        else:
+            return rpoB, invA, (average_read_length * number_of_reads) / 5000000
+
+
+
+def main():
+    ex_dir = os.path.dirname(os.path.realpath(__file__))
+    args = parse_args()
+    input_file = args.input_file
+    if input_file != 'None':
+        files = [input_file]
+    else:
+        extension = args.extension
+        inputdir = args.input_dir
+        files = [inputdir + '/'+ f for f in os.listdir(inputdir) if f.endswith(extension)]
+    report = args.report
+    mode = args.mode
+    f_invA = open(ex_dir + "/invA_mers_dict", "rb")
+    sets_dict_invA = pickle.load(f_invA)
+    f_invA.close()
+    allmers = sets_dict_invA['allmers']
+    uniqmers_I = sets_dict_invA['uniqmers_I']
+    uniqmers_IIa = sets_dict_invA['uniqmers_IIa']
+    uniqmers_IIb = sets_dict_invA['uniqmers_IIb']
+    uniqmers_IIIa = sets_dict_invA['uniqmers_IIIa']
+    uniqmers_IIIb = sets_dict_invA['uniqmers_IIIb']
+    uniqmers_IV = sets_dict_invA['uniqmers_IV']
+    uniqmers_VI = sets_dict_invA['uniqmers_VI']
+    uniqmers_VII = sets_dict_invA['uniqmers_VII']
+    uniqmers_VIII = sets_dict_invA['uniqmers_VIII']
+    uniqmers_bongori = sets_dict_invA['uniqmers_bongori']
+
+    f = open(ex_dir + "/rpoB_mers_dict", "rb")
+    sets_dict = pickle.load(f)
+    f.close()
+
+    allmers_rpoB = sets_dict['allmers']
+    uniqmers_bongori_rpoB = sets_dict['uniqmers_bongori']
+    uniqmers_S_enterica_rpoB = sets_dict['uniqmers_S_enterica']
+    uniqmers_Escherichia_rpoB = sets_dict['uniqmers_Escherichia']
+    uniqmers_Listeria_ss_rpoB = sets_dict['uniqmers_Listeria_ss']
+    uniqmers_Lmono_rpoB = sets_dict['uniqmers_L_mono']
+    #todo: run kmer_lists() once, create list of tuples containing data to be used fro different reports
+    if report == 'taxonomy':
+        print('file\trpoB\tinvA\texpected coverage')
+        for f in files:
+            locus_scores, coverages, reads = kmer_lists(f, 27,
+                                                        allmers, allmers_rpoB,
+                                                        uniqmers_bongori,
+                                                        uniqmers_I,
+                                                        uniqmers_IIa,
+                                                        uniqmers_IIb,
+                                                        uniqmers_IIIa,
+                                                        uniqmers_IIIb,
+                                                        uniqmers_IV,
+                                                        uniqmers_VI,
+                                                        uniqmers_VII,
+                                                        uniqmers_VIII,
+                                                        uniqmers_bongori_rpoB,
+                                                        uniqmers_S_enterica_rpoB,
+                                                        uniqmers_Escherichia_rpoB,
+                                                        uniqmers_Listeria_ss_rpoB,
+                                                        uniqmers_Lmono_rpoB,
+                                                        mode)
+            pretty_covs = [round(cov, 1) for cov in coverages]
+            report = report_taxon(pretty_covs, get_av_read_length(f), reads)
+            print(f.split('/')[-1] + '\t' + report[0][0] + '[' + str(report[0][1]) + ']' + '\t' + report[1][0] +
+                  '[' + str(report[1][1]) + ']' +
+                  '\t' + str(round(report[2], 1)))
+    else:
+        print(
+        'file\tListeria sensu stricto (rpoB)\tL. monocytogenes (rpoB)\tEscherichia spp. (rpoB)\tS. bongori (rpoB)\tS. enterica' +
+        '(rpoB)\tS. bongori (invA)\tsubsp. I (invA)\tsubsp. II (clade a: invA)\tsubsp. II' +
+        ' (clade b: invA)\tsubsp. IIIa (invA)\tsubsp. IIIb (invA)\tsubsp.IV (invA)\tsubsp. VI (invA)\tsubsp. VII (invA)' +
+        '\tsubsp. II (clade VIII : invA)')
+        if report == 'percentage':
+            for f in files:
+                locus_scores, coverages , reads = kmer_lists( f, 27,
+                           allmers,allmers_rpoB,
+                           uniqmers_bongori,
+                           uniqmers_I,
+                           uniqmers_IIa,
+                           uniqmers_IIb,
+                           uniqmers_IIIa,
+                           uniqmers_IIIb,
+                           uniqmers_IV,
+                           uniqmers_VI,
+                           uniqmers_VII,
+                           uniqmers_VIII,
+                           uniqmers_bongori_rpoB,
+                           uniqmers_S_enterica_rpoB,
+                           uniqmers_Escherichia_rpoB,
+                           uniqmers_Listeria_ss_rpoB,
+                           uniqmers_Lmono_rpoB,
+                           mode)
+                pretty_scores = [str(round(score)) for score in locus_scores]
+                print(f.split('/')[-1] +'\t' + '\t'.join(pretty_scores))
+        else:
+            for f in files:
+                locus_scores, coverages , reads = kmer_lists( f, 27,
+                           allmers,allmers_rpoB,
+                           uniqmers_bongori,
+                           uniqmers_I,
+                           uniqmers_IIa,
+                           uniqmers_IIb,
+                           uniqmers_IIIa,
+                           uniqmers_IIIb,
+                           uniqmers_IV,
+                           uniqmers_VI,
+                           uniqmers_VII,
+                           uniqmers_VIII,
+                           uniqmers_bongori_rpoB,
+                           uniqmers_S_enterica_rpoB,
+                           uniqmers_Escherichia_rpoB,
+                           uniqmers_Listeria_ss_rpoB,
+                           uniqmers_Lmono_rpoB,
+                           mode)
+                pretty_covs = [str(round(cov, 1)) for cov in coverages]
+                print(f.split('/')[-1] + '\t' + '\t'.join(pretty_covs))
+
+if __name__ == '__main__':
+    main()
+