Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.5.0/bin/dl_pdg_metadata.py @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 #!/usr/bin/env python3
2
3 # Kranti Konganti
4
5 import os
6 import shutil
7 import tempfile
8 import argparse
9 import inspect
10 import logging
11 import re
12 from urllib.request import urlopen
13 from html.parser import HTMLParser
14
15 # Set logging.f
16 logging.basicConfig(
17 format="\n" + "=" * 55 + "\n%(asctime)s - %(levelname)s\n" + "=" * 55 + "\n%(message)s\n",
18 level=logging.DEBUG,
19 )
20
21 # Multiple inheritence for pretty printing of help text.
22 class MultiArgFormatClasses(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter):
23 pass
24
25
26 # HTMLParser override class to get PDG release and latest Cluster .tsv file
27 class NCBIPathogensHTMLParser(HTMLParser):
28 def __init__(self, *, convert_charrefs: bool = ...) -> None:
29 super().__init__(convert_charrefs=convert_charrefs)
30 self.reset()
31 self.href_data = list()
32
33 def handle_data(self, data):
34 self.href_data.append(data)
35
36
37 def dl_pdg(**kwargs) -> None:
38 """
39 Method to save the PDG metadata file and
40 return the latest PDG release.
41 """
42 db_path, url, regex, suffix, overwrite, release = [kwargs[k] for k in kwargs.keys()]
43
44 if (db_path or url) == None:
45 logging.error("Please provide absolute UNIX path\n" + "to store the result DB flat files.")
46 exit(1)
47
48 if re.match(r"^PDG\d+\.\d+$", release):
49 url = re.sub("latest_snps", release.strip(), url)
50
51 html_parser = NCBIPathogensHTMLParser()
52 logging.info(f"Finding latest NCBI PDG release at:\n{url}")
53
54 with urlopen(url) as response:
55 with tempfile.NamedTemporaryFile(delete=False) as tmp_html_file:
56 shutil.copyfileobj(response, tmp_html_file)
57
58 with open(tmp_html_file.name, "r") as html:
59 html_parser.feed("".join(html.readlines()))
60
61 pdg_filename = re.search(regex, "".join(html_parser.href_data)).group(0)
62 pdg_release = pdg_filename.rstrip(suffix)
63 pdg_metadata_url = "/".join([url, pdg_filename])
64 pdg_release = pdg_filename.rstrip(suffix)
65 dest_dir = os.path.join(db_path, pdg_release)
66
67 logging.info(f"Found NCBI PDG file:\n{pdg_metadata_url}")
68
69 if (
70 not overwrite
71 and re.match(r".+?\.metadata\.tsv$", pdg_filename)
72 and os.path.exists(dest_dir)
73 ):
74 logging.error(f"DB path\n{dest_dir}\nalready exists. Please use -f to overwrite.")
75 exit(1)
76 elif overwrite and not re.match(r".+?\.reference_target\.cluster_list\.tsv$", pdg_filename):
77 shutil.rmtree(dest_dir, ignore_errors=True) if os.path.exists(dest_dir) else None
78 os.makedirs(dest_dir)
79 elif (
80 not overwrite
81 and re.match(r".+?\.metadata\.tsv$", pdg_filename)
82 and not os.path.exists(dest_dir)
83 ):
84 os.makedirs(dest_dir)
85
86 tsv_at = os.path.join(dest_dir, pdg_filename)
87 logging.info(f"Saving to:\n{tsv_at}")
88
89 with urlopen(pdg_metadata_url) as response:
90 with open(tsv_at, "w") as tsv:
91 tsv.writelines(response.read().decode("utf-8"))
92
93 html.close()
94 tmp_html_file.close()
95 os.unlink(tmp_html_file.name)
96 tsv.close()
97 response.close()
98
99 return tsv_at, dest_dir
100
101
102 def main() -> None:
103 """
104 This script is part of the `bettercallsal_db` Nextflow workflow and is only
105 tested on POSIX sytems.
106 It:
107 1. Downloads the latest NCBI Pathogens Release metadata file, which
108 looks like PDGXXXXXXXXXX.2504.metadata.csv and also the SNP cluster
109 information file which looks like PDGXXXXXXXXXX.2504.reference_target.cluster_list.tsv
110 2. Generates a new metadata file with only required information such as
111 computed_serotype, isolates GenBank or RefSeq downloadable genome FASTA
112 URL.
113 """
114
115 prog_name = os.path.basename(inspect.stack()[0].filename)
116
117 parser = argparse.ArgumentParser(
118 prog=prog_name, description=main.__doc__, formatter_class=MultiArgFormatClasses
119 )
120
121 # required = parser.add_argument_group("required arguments")
122
123 parser.add_argument(
124 "-db",
125 dest="db_path",
126 default=os.getcwd(),
127 required=False,
128 help="Absolute UNIX path to a path where all results files are\nstored.",
129 )
130 parser.add_argument(
131 "-f",
132 dest="overwrite_db",
133 default=False,
134 required=False,
135 action="store_true",
136 help="Force overwrite a PDG release directory at DB path\nmentioned with -db.",
137 )
138 parser.add_argument(
139 "-org",
140 dest="organism",
141 default="Salmonella",
142 required=False,
143 help="The organism to create the DB flat files\nfor.",
144 )
145 parser.add_argument(
146 "-rel",
147 dest="release",
148 default=False,
149 required=False,
150 help="If you get a 404 error, try mentioning the actual release identifier.\n"
151 + "Ex: For Salmonella, you can get the release identifier by going to:\n"
152 + " https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella\n"
153 + "Ex: If you want metadata beloginging to release PDG000000002.2507, then you\n"
154 + " would use this command-line option as:\n -rel PDG000000002.2507",
155 )
156
157 args = parser.parse_args()
158 db_path = args.db_path
159 org = args.organism
160 overwrite = args.overwrite_db
161 release = args.release
162 ncbi_pathogens_loc = "/".join(
163 ["https://ftp.ncbi.nlm.nih.gov/pathogen/Results", org, "latest_snps"]
164 )
165
166 if not db_path:
167 db_path = os.getcwd()
168
169 # Save metadata
170 file, dest_dir = dl_pdg(
171 db_path=db_path,
172 url="/".join([ncbi_pathogens_loc, "Metadata"]),
173 regex=re.compile(r"PDG\d+\.\d+\.metadata\.tsv"),
174 suffix=".metadata.tsv",
175 overwrite=overwrite,
176 release=release,
177 )
178
179 # Save cluster to target mapping
180 dl_pdg(
181 db_path=db_path,
182 url="/".join([ncbi_pathogens_loc, "Clusters"]),
183 regex=re.compile(r"PDG\d+\.\d+\.reference_target\.cluster_list\.tsv"),
184 suffix="reference_target\.cluster_list\.tsv",
185 overwrite=overwrite,
186 release=release,
187 )
188
189 # Create accs.txt for dataformat to fetch required ACC fields
190 accs_file = os.path.join(dest_dir, "accs_all.txt")
191 with open(file, "r") as pdg_metadata_fh:
192 with open(accs_file, "w") as accs_fh:
193 for line in pdg_metadata_fh.readlines():
194 if re.match(r"^#", line) or line in ["\n", "\n\r", "\r"]:
195 continue
196 cols = line.strip().split("\t")
197 asm_acc = cols[9]
198 accs_fh.write(f"{asm_acc}\n") if (asm_acc != "NULL") else None
199 accs_fh.close()
200 pdg_metadata_fh.close()
201
202 logging.info("Finished writing accessions for dataformat tool.")
203
204
205 if __name__ == "__main__":
206 main()