Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/bin/index_pdg_metadata.py @ 0:0a8dda29956e draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 #!/usr/bin/env python3
2
3 # Kranti Konganti
4
5 import argparse
6 import inspect
7 import logging
8 import os
9 import pickle
10 import pprint
11 import re
12 from collections import defaultdict
13
14
15 # Multiple inheritence for pretty printing of help text.
16 class MultiArgFormatClasses(
17 argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter
18 ):
19 pass
20
21
22 # Main
23 def main() -> None:
24 """
25 This script works only in the context of `bettercallsal_db` Nextflow workflow.
26 It takes an UNIX path to directory containing the following files:
27 1. PDG metadata file (Ex: `PDG000000043.204.metadata.tsv`)
28 2. PDG SNP Cluster metadata file (Ex: `PDG000000043.204.reference_target.cluster_list.tsv`)
29 3. A list of possibly downloadable assembly accessions (one per line) from the metadata file.
30 and then generates a pickled file with relevant metadata columns mentioned with the -cols option.
31 """
32
33 # Set logging.
34 logging.basicConfig(
35 format="\n"
36 + "=" * 55
37 + "\n%(asctime)s - %(levelname)s\n"
38 + "=" * 55
39 + "\n%(message)s\n\n",
40 level=logging.DEBUG,
41 )
42
43 # Debug print.
44 ppp = pprint.PrettyPrinter(width=55)
45 prog_name = os.path.basename(inspect.stack()[0].filename)
46
47 parser = argparse.ArgumentParser(
48 prog=prog_name, description=main.__doc__, formatter_class=MultiArgFormatClasses
49 )
50
51 required = parser.add_argument_group("required arguments")
52
53 required.add_argument(
54 "-pdg_dir",
55 dest="pdg_dir",
56 default=False,
57 required=True,
58 help="Absolute UNIX path to directory containing the following files.\nEx:"
59 + "\n1. PDG000000043.204.metadata.tsv"
60 + "\n2. PDG000000043.204.reference_target.cluster_list.tsv"
61 + "\n3. A file of assembly accessions, one per line parsed out from"
62 + "\n the metadata file.",
63 )
64 parser.add_argument(
65 "-mlst",
66 dest="mlst_results",
67 required=False,
68 help="Absolute UNIX path to MLST results file\nIf MLST results exists for a accession, they"
69 + "\nwill be included in the index.",
70 )
71 parser.add_argument(
72 "-pdg_meta_pat",
73 dest="pdg_meta_pat",
74 default="PDG\d+\.\d+\.metadata\.tsv",
75 required=False,
76 help="The pattern to be used to search for PDG metadata\nfile.",
77 )
78 parser.add_argument(
79 "-pdg_snp_meta_pat",
80 dest="pdg_snp_meta_pat",
81 default="PDG\d+\.\d+\.reference\_target\.cluster\_list\.tsv",
82 required=False,
83 help="The pattern to be used to search for PDG SNP Cluster metadata\nfile.",
84 )
85 parser.add_argument(
86 "-pdg_accs_filename_pat",
87 dest="pdg_accs_fn_pat",
88 default="accs_all.txt",
89 required=False,
90 help="The filename to look for where all the parsed GC[AF] accessions are stored,\n"
91 + "one per line.",
92 )
93 parser.add_argument(
94 "-cols",
95 dest="metadata_cols",
96 default="epi_type,collected_by,collection_date,host,"
97 + "\nhost_disease,isolation_source,outbreak,sample_name,scientific_name,serovar,"
98 + "\nsource_type,strain,computed_types,target_acc,geo_loc_name",
99 required=False,
100 help="The data in these metadata columns will be indexed for each\nisolate.",
101 )
102 parser.add_argument(
103 "-fs",
104 dest="force_write_pick",
105 action="store_true",
106 required=False,
107 help="By default, when -s flag is on, the pickle file named *.IDXD_PDG_METAD.pickle"
108 + "\nis written to CWD. If the file exists, the program will not overwrite"
109 + "\nand exit. Use -fs option to overwrite.",
110 )
111 parser.add_argument(
112 "-op",
113 dest="out_prefix",
114 default="IDXD_PDG_METAD",
115 help="Set the output file prefix for indexed PDG metadata.",
116 )
117 parser.add_argument(
118 "-pfs",
119 dest="pdg_meta_fs",
120 default="\t",
121 help="Change the field separator of the PDG metadata file.",
122 )
123
124 args = parser.parse_args()
125 pdg_dir = os.path.abspath(args.pdg_dir)
126 mcols = args.metadata_cols
127 f_write_pick = args.force_write_pick
128 out_prefix = args.out_prefix
129 pdg_meta_fs = args.pdg_meta_fs
130 mlst_res = args.mlst_results
131 acc_pat = re.compile(r"^GC[AF]\_\d+\.?\d*")
132 mcols_pat = re.compile(r"[\w+\,]")
133 pdg_meta_pat = re.compile(f"{args.pdg_meta_pat}")
134 pdg_snp_meta_pat = re.compile(f"{args.pdg_snp_meta_pat}")
135 pdg_accs_fn_pat = re.compile(f"{args.pdg_accs_fn_pat}")
136 target_acc_col = 41
137 acc_col = 9
138 num_accs_check = list()
139 mlst_sts = dict()
140 acceptable_num_mlst_cols = 10
141 mlst_st_col = 2
142 mlst_acc_col = 0
143
144 # Basic checks
145
146 if os.path.exists(pdg_dir) and os.path.isdir(pdg_dir):
147 pdg_meta_file = [f for f in os.listdir(pdg_dir) if pdg_meta_pat.match(f)]
148 pdg_snp_meta_file = [
149 f for f in os.listdir(pdg_dir) if pdg_snp_meta_pat.match(f)
150 ]
151 pdg_acc_all = [f for f in os.listdir(pdg_dir) if pdg_accs_fn_pat.match(f)]
152 req_files = [len(pdg_meta_file), len(pdg_snp_meta_file), len(pdg_acc_all)]
153 if any(x > 1 for x in req_files):
154 logging.error(
155 f"Directory {os.path.basename(pdg_dir)} contains"
156 + "\ncontains mulitple files matching the search pattern."
157 )
158 exit(1)
159 elif any(x == 0 for x in req_files):
160 logging.error(
161 f"Directory {os.path.basename(pdg_dir)} does not contain"
162 + "\nany files matching the following file patterns:"
163 + f"\n{pdg_meta_pat.pattern}"
164 + f"\n{pdg_snp_meta_pat.pattern}"
165 + f"\n{pdg_accs_fn_pat.pattern}"
166 )
167 exit(1)
168 pdg_meta_file = os.path.join(pdg_dir, "".join(pdg_meta_file))
169 pdg_snp_meta_file = os.path.join(pdg_dir, "".join(pdg_snp_meta_file))
170 pdg_acc_all = os.path.join(pdg_dir, "".join(pdg_acc_all))
171 else:
172 logging.error(f"Directory path {pdg_dir} does not exist.")
173 exit(1)
174
175 if mlst_res and not (os.path.exists(mlst_res) or os.path.getsize(mlst_res) > 0):
176 logging.error(
177 f"Requested to index MLST results. but the file {os.path.basename(mlst_res)}"
178 + "does not exist or the file is empty."
179 )
180 exit(1)
181 elif mlst_res:
182 with open(mlst_res, "r") as mlst_res_fh:
183 header = mlst_res_fh.readline()
184 mlst_res_has_10_cols = False
185
186 for line in mlst_res_fh:
187 cols = line.strip().split("\t")
188 acc = acc_pat.findall(cols[mlst_acc_col])
189 if len(acc) > 1:
190 logging.error(
191 f"Found more than 1 accession in column:\ncols[mlst_acc_col]\n"
192 )
193 exit(1)
194 else:
195 acc = "".join(acc)
196 if len(cols) == acceptable_num_mlst_cols and re.match(
197 r"\d+|\-", cols[mlst_st_col]
198 ):
199 mlst_res_has_10_cols = True
200 if re.match(r"\-", cols[mlst_st_col]):
201 mlst_sts[acc] = "NULL"
202 else:
203 mlst_sts[acc] = cols[mlst_st_col]
204
205 if not mlst_res_has_10_cols:
206 logging.error(
207 "Requested to incorporate MLST ST's but file"
208 + f"\n{os.path.basename(mlst_res)}"
209 + "\ndoes not have 10 columns in all rows."
210 )
211 exit(1)
212
213 mlst_res_fh.close()
214
215 with open(pdg_acc_all, "r") as pdg_acc_all_fh:
216 for a in pdg_acc_all_fh.readlines():
217 num_accs_check.append(a.strip())
218
219 if not mcols_pat.match(mcols):
220 logging.error(
221 f"Supplied columns' names should only be"
222 + "\nalphanumeric (including _) separated by a comma."
223 )
224 exit(1)
225 else:
226 mcols = re.sub("\n", "", mcols).split(",")
227
228 if (
229 pdg_snp_meta_file
230 and os.path.exists(pdg_snp_meta_file)
231 and os.path.getsize(pdg_snp_meta_file) > 0
232 ):
233 acc2snp = defaultdict()
234 acc2meta = defaultdict(defaultdict)
235 init_pickled_sero = os.path.join(os.getcwd(), out_prefix + ".pickle")
236
237 if (
238 os.path.exists(init_pickled_sero)
239 and os.path.getsize(init_pickled_sero)
240 and not f_write_pick
241 ):
242 logging.error(
243 f"File {os.path.basename(init_pickled_sero)} already exists in\n{os.getcwd()}\n"
244 + "Use -fs to force overwrite it."
245 )
246 exit(1)
247
248 with open(pdg_snp_meta_file, "r") as snp_meta:
249 header = snp_meta.readline()
250 skipped_acc2snp = set()
251 for line in snp_meta:
252 cols = line.strip().split(pdg_meta_fs)
253 if not 4 <= len(cols) < 5:
254 logging.error(
255 f"The metadata file {pdg_snp_meta_file} is malformed.\n"
256 + f"Expected 4 columns. Got {len(cols)} columns.\n"
257 )
258 exit(1)
259
260 if re.match("NULL", cols[3]):
261 skipped_acc2snp.add(
262 f"Isolate {cols[1]} has no genome accession: {cols[3]}"
263 )
264 elif not acc_pat.match(cols[3]):
265 logging.error(
266 f"Did not find accession in either field number 4\n"
267 + "or field number 10 of column 4."
268 + f"\nLine: {line}"
269 )
270 exit(1)
271 elif not re.match("NULL", cols[3]):
272 acc2snp[cols[3]] = cols[0]
273
274 if len(skipped_acc2snp) > 0:
275 logging.info(
276 f"While indexing\n{os.path.basename(pdg_snp_meta_file)},"
277 + "\nthese isolates were skipped:\n\n"
278 + "\n".join(skipped_acc2snp)
279 )
280
281 with open(pdg_meta_file, "r") as pdg_meta:
282 header = pdg_meta.readline().strip().split(pdg_meta_fs)
283 user_req_cols = [
284 mcol_i for mcol_i, mcol in enumerate(header) if mcol in mcols
285 ]
286 cols_not_found = [mcol for mcol in mcols if mcol not in header]
287 null_wgs_accs = set()
288 if len(cols_not_found) > 0:
289 logging.error(
290 f"The following columns do not exist in the"
291 + f"\nmetadata file [ {os.path.basename(pdg_meta_file)} ]:\n"
292 + "".join(cols_not_found)
293 )
294 exit(1)
295
296 for line in pdg_meta.readlines():
297 cols = line.strip().split(pdg_meta_fs)
298 pdg_assm_acc = cols[acc_col]
299 if not acc_pat.match(pdg_assm_acc):
300 null_wgs_accs.add(
301 f"Isolate {cols[target_acc_col]} has no genome accession: {pdg_assm_acc}"
302 )
303 continue
304
305 if pdg_assm_acc in mlst_sts.keys():
306 acc2meta[pdg_assm_acc].setdefault("mlst_sequence_type", []).append(
307 str(mlst_sts[pdg_assm_acc])
308 )
309
310 for col in user_req_cols:
311 acc2meta[pdg_assm_acc].setdefault(header[col], []).append(
312 str(cols[col])
313 )
314
315 if len(null_wgs_accs) > 0:
316 logging.info(
317 f"While indexing\n{os.path.basename(pdg_meta_file)},"
318 + "\nthese isolates were skipped:\n\n"
319 + "\n".join(null_wgs_accs)
320 )
321
322 with open(init_pickled_sero, "wb") as write_pickled_sero:
323 pickle.dump(file=write_pickled_sero, obj=acc2meta)
324
325 if len(num_accs_check) != len(acc2meta.keys()):
326 logging.error(
327 "Failed the accession count check."
328 + f"\nExpected {len(num_accs_check)} accessions but got {len(acc2meta.keys())}."
329 )
330 exit(1)
331 else:
332 logging.info(
333 f"Number of valid accessions: {len(num_accs_check)}"
334 + f"\nNumber of accessions indexed: {len(acc2meta.keys())}"
335 + f"\nNumber of accessions participating in any of the SNP Clusters: {len(acc2snp.keys())}"
336 + f"\n\nCreated the pickle file for\n{os.path.basename(pdg_meta_file)}."
337 + "\nThis was the only requested function."
338 )
339
340 snp_meta.close()
341 write_pickled_sero.close()
342 exit(0)
343 elif pdg_meta_file and not (
344 os.path.exists(pdg_meta_file) and os.path.getsize(pdg_meta_file) > 0
345 ):
346 logging.error(
347 "Requested to create pickle from metadata, but\n"
348 + f"the file, {os.path.basename(pdg_meta_file)} is empty or\ndoes not exist!"
349 )
350 exit(1)
351
352 pdg_acc_all_fh.close()
353 snp_meta.close()
354 pdg_meta.close()
355 write_pickled_sero.close()
356
357
358 if __name__ == "__main__":
359 main()