Mercurial > repos > iss > eurl_vtec_wgs_pt

comparison scripts/ReMatCh/rematch.py @ 0:c6bab5103a14 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
author iss
date Mon, 21 Mar 2022 15:23:09 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:c6bab5103a14
1 #!/usr/bin/env python3
2
3 # -*- coding: utf-8 -*-
4
5 """
6 rematch.py - Reads mapping against target sequences, checking mapping
7 and consensus sequences production
8 <https://github.com/B-UMMI/ReMatCh/>
9
10 Copyright (C) 2019 Miguel Machado <mpmachado@medicina.ulisboa.pt>
11
12 Last modified: August 08, 2019
13
14 This program is free software: you can redistribute it and/or modify
15 it under the terms of the GNU General Public License as published by
16 the Free Software Foundation, either version 3 of the License, or
17 (at your option) any later version.
18
19 This program is distributed in the hope that it will be useful,
20 but WITHOUT ANY WARRANTY; without even the implied warranty of
21 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22 GNU General Public License for more details.
23
24 You should have received a copy of the GNU General Public License
25 along with this program. If not, see <http://www.gnu.org/licenses/>.
26 """
27
28 import os
29 import sys
30 import time
31 import argparse
32
33 try:
34 from __init__ import __version__
35
36 import modules.utils as utils
37 import modules.seqFromWebTaxon as seq_from_web_taxon
38 import modules.download as download
39 import modules.rematch_module as rematch_module
40 import modules.checkMLST as check_mlst
41 except ImportError:
42 from ReMatCh.__init__ import __version__
43
44 from ReMatCh.modules import utils as utils
45 from ReMatCh.modules import seqFromWebTaxon as seq_from_web_taxon
46 from ReMatCh.modules import download as download
47 from ReMatCh.modules import rematch_module as rematch_module
48 from ReMatCh.modules import checkMLST as check_mlst
49
50
51 def search_fastq_files(directory):
52 files_extensions = ['.fastq.gz', '.fq.gz']
53 pair_end_files_separation = [['_R1_001.f', '_R2_001.f'], ['_1.f', '_2.f']]
54
55 list_ids = {}
56 directories = [d for d in os.listdir(directory) if
57 not d.startswith('.') and os.path.isdir(os.path.join(directory, d, ''))]
58 for directory_found in directories:
59 if directory_found != 'pubmlst':
60 directory_path = os.path.join(directory, directory_found, '')
61
62 fastq_found = []
63 files = [f for f in os.listdir(directory_path) if
64 not f.startswith('.') and os.path.isfile(os.path.join(directory_path, f))]
65 for file_found in files:
66 if file_found.endswith(tuple(files_extensions)):
67 fastq_found.append(file_found)
68
69 if len(fastq_found) == 1:
70 list_ids[directory_found] = [os.path.join(directory_path, f) for f in fastq_found]
71 elif len(fastq_found) >= 2:
72 file_pair = []
73
74 # Search pairs
75 for pe_separation in pair_end_files_separation:
76 for fastq in fastq_found:
77 if pe_separation[0] in fastq or pe_separation[1] in fastq:
78 file_pair.append(fastq)
79
80 if len(file_pair) == 2:
81 break
82 else:
83 file_pair = []
84
85 # Search single
86 if len(file_pair) == 0:
87 for pe_separation in pair_end_files_separation:
88 for fastq in fastq_found:
89 if pe_separation[0] not in fastq or pe_separation[1] not in fastq:
90 file_pair.append(fastq)
91
92 if len(file_pair) >= 1:
93 file_pair = file_pair[0]
94
95 if len(file_pair) >= 1:
96 list_ids[directory_found] = [os.path.join(directory_path, f) for f in file_pair]
97
98 return list_ids
99
100
101 def get_list_ids_from_file(file_list_ids):
102 list_ids = []
103
104 with open(file_list_ids, 'rtU') as lines:
105 for line in lines:
106 line = line.rstrip('\r\n')
107 if len(line) > 0:
108 list_ids.append(line)
109
110 if len(list_ids) == 0:
111 sys.exit('No runIDs were found in ' + file_list_ids)
112
113 return list_ids
114
115
116 def get_taxon_run_ids(taxon_name, outputfile):
117 seq_from_web_taxon.run_seq_from_web_taxon(taxon_name, outputfile, True, True, True, False)
118
119 run_ids = []
120 with open(outputfile, 'rtU') as reader:
121 for line in reader:
122 line = line.rstrip('\r\n')
123 if len(line) > 0:
124 if not line.startswith('#'):
125 line = line.split('\t')
126 run_ids.append(line[0])
127
128 return run_ids
129
130
131 def get_list_ids(workdir, file_list_ids, taxon_name):
132 searched_fastq_files = False
133 list_ids = []
134 if file_list_ids is None and taxon_name is None:
135 list_ids = search_fastq_files(workdir)
136 searched_fastq_files = True
137 elif file_list_ids is not None:
138 list_ids = get_list_ids_from_file(os.path.abspath(file_list_ids))
139 elif taxon_name is not None and file_list_ids is None:
140 list_ids = get_taxon_run_ids(taxon_name, os.path.join(workdir, 'IDs_list.seqFromWebTaxon.tab'))
141
142 if len(list_ids) == 0:
143 sys.exit('No IDs were found')
144 return list_ids, searched_fastq_files
145
146
147 def format_gene_info(gene_specific_info, minimum_gene_coverage, minimum_gene_identity, reported_data_type, summary,
148 sample, genes_present):
149 info = None
150 if gene_specific_info['gene_coverage'] >= minimum_gene_coverage and \
151 gene_specific_info['gene_identity'] >= minimum_gene_identity:
152 if summary and sample not in genes_present:
153 genes_present[sample] = {}
154
155 if gene_specific_info['gene_number_positions_multiple_alleles'] == 0:
156 s = str(gene_specific_info[reported_data_type])
157 info = str(s)
158 if summary:
159 genes_present[sample][gene_specific_info['header']] = str(s)
160 else:
161 s = 'multiAlleles_' + str(gene_specific_info[reported_data_type])
162 info = str(s)
163 if summary:
164 genes_present[sample][gene_specific_info['header']] = str(s)
165 else:
166 info = 'absent_' + str(gene_specific_info[reported_data_type])
167
168 return info, genes_present
169
170
171 def write_data_by_gene(gene_list_reference, minimum_gene_coverage, sample, data_by_gene, outdir, time_str, run_times,
172 minimum_gene_identity, reported_data_type, summary, genes_present):
173 combined_report = \
174 os.path.join(outdir,
175 'combined_report.data_by_gene.' + run_times + '.' + reported_data_type + '.' + time_str + '.tab')
176
177 if reported_data_type == 'coverage_depth':
178 reported_data_type = 'gene_mean_read_coverage'
179 elif reported_data_type == 'sequence_coverage':
180 reported_data_type = 'gene_coverage'
181
182 combined_report_exist = os.path.isfile(combined_report)
183 with open(combined_report, 'at') as writer:
184 seq_list = sorted(gene_list_reference.keys())
185 if not combined_report_exist:
186 writer.write('#sample' + '\t' + '\t'.join([gene_list_reference[seq] for seq in seq_list]) + '\n')
187
188 results = {}
189 headers = []
190 for i in data_by_gene:
191 results[data_by_gene[i]['header']], genes_present = format_gene_info(data_by_gene[i], minimum_gene_coverage,
192 minimum_gene_identity,
193 reported_data_type, summary, sample,
194 genes_present)
195 headers.append(data_by_gene[i]['header'])
196
197 if len(headers) != gene_list_reference:
198 for gene in gene_list_reference:
199 if gene not in headers:
200 results[gene] = 'NA'
201
202 writer.write(sample + '\t' + '\t'.join([results[seq] for seq in seq_list]) + '\n')
203
204 return genes_present
205
206
207 def write_sample_report(sample, outdir, time_str, file_size, run_successfully_fastq, run_successfully_rematch_first,
208 run_successfully_rematch_second, time_taken_fastq, time_taken_rematch_first,
209 time_taken_rematch_second, time_taken_sample, sequencing_information, sample_data_general_first,
210 sample_data_general_second, fastq_used):
211 sample_report = os.path.join(outdir, 'sample_report.' + time_str + '.tab')
212 report_exist = os.path.isfile(sample_report)
213
214 header_general = ['sample', 'sample_run_successfully', 'sample_run_time', 'files_size', 'download_run_successfully',
215 'download_run_time', 'rematch_run_successfully_first', 'rematch_run_time_first',
216 'rematch_run_successfully_second', 'rematch_run_time_second']
217 header_data_general = ['number_absent_genes', 'number_genes_multiple_alleles', 'mean_sample_coverage']
218 header_sequencing = ['run_accession', 'instrument_platform', 'instrument_model', 'library_layout', 'library_source',
219 'extra_run_accession', 'nominal_length', 'read_count', 'base_count', 'date_download']
220
221 with open(sample_report, 'at') as writer:
222 if not report_exist:
223 writer.write('#' + '\t'.join(header_general) + '\t' + '_first\t'.join(header_data_general) + '_first\t' +
224 '_second\t'.join(header_data_general) + '_second\t' + '\t'.join(header_sequencing) + '\t' +
225 'fastq_used' + '\n')
226
227 writer.write('\t'.join([sample,
228 str(all([run_successfully_fastq is not False,
229 run_successfully_rematch_first is not False,
230 run_successfully_rematch_second is not False])),
231 str(time_taken_sample),
232 str(file_size),
233 str(run_successfully_fastq),
234 str(time_taken_fastq),
235 str(run_successfully_rematch_first),
236 str(time_taken_rematch_first),
237 str(run_successfully_rematch_second),
238 str(time_taken_rematch_second)]) +
239 '\t' + '\t'.join([str(sample_data_general_first[i]) for i in header_data_general]) +
240 '\t' + '\t'.join([str(sample_data_general_second[i]) for i in header_data_general]) +
241 '\t' + '\t'.join([str(sequencing_information[i]) for i in header_sequencing]) +
242 '\t' + ','.join(fastq_used) + '\n')
243
244
245 def concatenate_extra_seq_2_consensus(consensus_sequence, reference_sequence, extra_seq_length, outdir):
246 reference_dict, ignore, ignore = rematch_module.get_sequence_information(reference_sequence, extra_seq_length)
247 consensus_dict, genes, ignore = rematch_module.get_sequence_information(consensus_sequence, 0)
248 number_consensus_with_sequences = 0
249 for k, values_consensus in list(consensus_dict.items()):
250 for values_reference in list(reference_dict.values()):
251 if values_reference['header'] == values_consensus['header']:
252 if len(set(consensus_dict[k]['sequence'])) > 1:
253 number_consensus_with_sequences += 1
254 if extra_seq_length <= len(values_reference['sequence']):
255 right_extra_seq = \
256 '' if extra_seq_length == 0 else values_reference['sequence'][-extra_seq_length:]
257 consensus_dict[k]['sequence'] = \
258 values_reference['sequence'][:extra_seq_length] + \
259 consensus_dict[k]['sequence'] + \
260 right_extra_seq
261 consensus_dict[k]['length'] += extra_seq_length + len(right_extra_seq)
262
263 consensus_concatenated = os.path.join(outdir, 'consensus_concatenated_extraSeq.fasta')
264 with open(consensus_concatenated, 'wt') as writer:
265 for i in consensus_dict:
266 writer.write('>' + consensus_dict[i]['header'] + '\n')
267 fasta_sequence_lines = rematch_module.chunkstring(consensus_dict[i]['sequence'], 80)
268 for line in fasta_sequence_lines:
269 writer.write(line + '\n')
270
271 return consensus_concatenated, genes, consensus_dict, number_consensus_with_sequences
272
273
274 def clean_headers_reference_file(reference_file, outdir, extra_seq):
275 problematic_characters = ["|", " ", ",", ".", "(", ")", "'", "/", ":"]
276 print('Checking if reference sequences contain ' + str(problematic_characters) + '\n')
277 # headers_changed = False
278 new_reference_file = str(reference_file)
279 sequences, genes, headers_changed = rematch_module.get_sequence_information(reference_file, extra_seq)
280 if headers_changed:
281 print('At least one of the those characters was found. Replacing those with _' + '\n')
282 new_reference_file = \
283 os.path.join(outdir, os.path.splitext(os.path.basename(reference_file))[0] + '.headers_renamed.fasta')
284 with open(new_reference_file, 'wt') as writer:
285 for i in sequences:
286 writer.write('>' + sequences[i]['header'] + '\n')
287 fasta_sequence_lines = rematch_module.chunkstring(sequences[i]['sequence'], 80)
288 for line in fasta_sequence_lines:
289 writer.write(line + '\n')
290 return new_reference_file, genes, sequences
291
292
293 def write_mlst_report(sample, run_times, consensus_type, st, alleles_profile, loci_order, outdir, time_str):
294 mlst_report = os.path.join(outdir, 'mlst_report.' + time_str + '.tab')
295 mlst_report_exist = os.path.isfile(mlst_report)
296 with open(mlst_report, 'at') as writer:
297 if not mlst_report_exist:
298 writer.write('\t'.join(['#sample', 'ReMatCh_run', 'consensus_type', 'ST'] + loci_order) + '\n')
299 writer.write('\t'.join([sample, run_times, consensus_type, str(st)] + alleles_profile.split(',')) + '\n')
300
301
302 def run_get_st(sample, mlst_dicts, consensus_sequences, mlst_consensus, run_times, outdir, time_str):
303 if mlst_consensus == 'all':
304 for consensus_type in consensus_sequences:
305 print('Searching MLST for ' + consensus_type + ' consensus')
306 st, alleles_profile = check_mlst.get_st(mlst_dicts, consensus_sequences[consensus_type])
307 write_mlst_report(sample, run_times, consensus_type, st, alleles_profile, mlst_dicts[2], outdir, time_str)
308 print('ST found: ' + str(st) + ' (' + alleles_profile + ')')
309 else:
310 st, alleles_profile = check_mlst.get_st(mlst_dicts, consensus_sequences[mlst_consensus])
311 write_mlst_report(sample, run_times, mlst_consensus, st, alleles_profile, mlst_dicts[2], outdir, time_str)
312 print('ST found for ' + mlst_consensus + ' consensus: ' + str(st) + ' (' + alleles_profile + ')')
313
314
315 def write_summary_report(outdir, reported_data_type, time_str, gene_list_reference, genes_present):
316 with open(os.path.join(outdir,
317 'summary.{reported_data_type}.{time_str}.tab'.format(reported_data_type=reported_data_type,
318 time_str=time_str)), 'wt') as writer:
319 seq_list = []
320 for info in list(genes_present.values()):
321 seq_list.extend(list(info.keys()))
322 seq_list = list(set(seq_list))
323 writer.write('#sample' + '\t' + '\t'.join([gene_list_reference[seq] for seq in sorted(seq_list)]) + '\n')
324 for sample, info in list(genes_present.items()):
325 data = []
326 for seq in sorted(seq_list):
327 if seq in info:
328 data.append(info[seq])
329 else:
330 data.append('NF')
331 writer.write(sample + '\t' + '\t'.join(data) + '\n')
332
333
334 def run_rematch(args):
335 workdir = os.path.abspath(args.workdir)
336 if not os.path.isdir(workdir):
337 os.makedirs(workdir)
338
339 aspera_key = os.path.abspath(args.asperaKey.name) if args.asperaKey is not None else None
340
341 # Start logger
342 logfile, time_str = utils.start_logger(workdir)
343
344 # Get general information
345 script_path = utils.general_information(logfile, __version__, workdir, time_str, args.doNotUseProvidedSoftware,
346 aspera_key, args.downloadCramBam, args.SRA, args.SRAopt)
347
348 # Set list_ids
349 list_ids, searched_fastq_files = get_list_ids(workdir, args.listIDs.name if args.listIDs is not None else None,
350 args.taxon)
351
352 mlst_sequences = None
353 mlst_dicts = None
354 if args.mlst is not None:
355 time_taken_pub_mlst, mlst_dicts, mlst_sequences = check_mlst.download_pub_mlst_xml(args.mlst,
356 args.mlstSchemaNumber,
357 workdir)
358 args.softClip_recodeRun = 'first'
359
360 if args.reference is None:
361 if args.mlst is not None:
362 reference_file = check_mlst.check_existing_schema(args.mlst, args.mlstSchemaNumber, script_path)
363 args.extraSeq = 200
364 if reference_file is None:
365 print('It was not found provided MLST scheme sequences for ' + args.mlst)
366 print('Trying to obtain reference MLST sequences from PubMLST')
367 if len(mlst_sequences) > 0:
368 reference_file = check_mlst.write_mlst_reference(args.mlst, mlst_sequences, workdir, time_str)
369 args.extraSeq = 0
370 else:
371 sys.exit('It was not possible to download MLST sequences from PubMLST!')
372 else:
373 print('Using provided scheme as referece: ' + reference_file)
374 else:
375 sys.exit('Need to provide at least one of the following options: "--reference" and "--mlst"')
376 else:
377 reference_file = os.path.abspath(args.reference.name)
378
379 # Run ReMatCh for each sample
380 print('\n' + 'STARTING ReMatCh' + '\n')
381
382 # Clean sequences headers
383 reference_file, gene_list_reference, reference_dict = clean_headers_reference_file(reference_file, workdir,
384 args.extraSeq)
385
386 if args.mlst is not None:
387 problem_genes = False
388 for header in mlst_sequences:
389 if header not in gene_list_reference:
390 print('MLST gene {header} not found between reference sequences'.format(header=header))
391 problem_genes = True
392 if problem_genes:
393 sys.exit('Missing MLST genes from reference sequences (at least sequences names do not match)!')
394
395 if len(gene_list_reference) == 0:
396 sys.exit('No sequences left')
397
398 # To use in combined report
399
400 number_samples_successfully = 0
401 genes_present_coverage_depth = {}
402 genes_present_sequence_coverage = {}
403 for sample in list_ids:
404 sample_start_time = time.time()
405 print('\n\n' + 'Sample ID: ' + sample)
406
407 # Create sample outdir
408 sample_outdir = os.path.join(workdir, sample, '')
409 if not os.path.isdir(sample_outdir):
410 os.mkdir(sample_outdir)
411
412 run_successfully_fastq = None
413 time_taken_fastq = 0
414 sequencing_information = {'run_accession': None, 'instrument_platform': None, 'instrument_model': None,
415 'library_layout': None, 'library_source': None, 'extra_run_accession': None,
416 'nominal_length': None, 'read_count': None, 'base_count': None, 'date_download': None}
417 if not searched_fastq_files:
418 # Download Files
419 time_taken_fastq, run_successfully_fastq, fastq_files, sequencing_information = \
420 download.run_download(sample, args.downloadLibrariesType, aspera_key, sample_outdir,
421 args.downloadCramBam, args.threads, args.downloadInstrumentPlatform, args.SRA,
422 args.SRAopt)
423 else:
424 fastq_files = list_ids[sample]
425
426 file_size = None
427
428 run_successfully_rematch_first = None
429 run_successfully_rematch_second = None
430 time_taken_rematch_first = 0
431 time_taken_rematch_second = 0
432 sample_data_general_first = None
433 sample_data_general_second = None
434 if run_successfully_fastq is not False:
435 file_size = sum(os.path.getsize(fastq) for fastq in fastq_files)
436 # Run ReMatCh
437 time_taken_rematch_first, run_successfully_rematch_first, data_by_gene, sample_data_general_first, \
438 consensus_files, consensus_sequences = \
439 rematch_module.run_rematch_module(sample, fastq_files, reference_file, args.threads, sample_outdir,
440 args.extraSeq, args.minCovPresence, args.minCovCall,
441 args.minFrequencyDominantAllele, args.minGeneCoverage,
442 args.debug, args.numMapLoc, args.minGeneIdentity,
443 'first', args.softClip_baseQuality, args.softClip_recodeRun,
444 reference_dict, args.softClip_cigarFlagRecode,
445 args.bowtieAlgo, args.bowtieOPT,
446 gene_list_reference, args.notWriteConsensus, clean_run=True)
447 if run_successfully_rematch_first:
448 if args.mlst is not None and (args.mlstRun == 'first' or args.mlstRun == 'all'):
449 run_get_st(sample, mlst_dicts, consensus_sequences, args.mlstConsensus, 'first', workdir, time_str)
450 genes_present_coverage_depth = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample,
451 data_by_gene, workdir, time_str, 'first_run',
452 args.minGeneIdentity, 'coverage_depth', args.summary,
453 genes_present_coverage_depth)
454 if args.reportSequenceCoverage:
455 genes_present_sequence_coverage = write_data_by_gene(gene_list_reference, args.minGeneCoverage,
456 sample, data_by_gene, workdir, time_str,
457 'first_run', args.minGeneIdentity,
458 'sequence_coverage', args.summary,
459 genes_present_sequence_coverage)
460 if args.doubleRun:
461 rematch_second_outdir = os.path.join(sample_outdir, 'rematch_second_run', '')
462 if not os.path.isdir(rematch_second_outdir):
463 os.mkdir(rematch_second_outdir)
464 consensus_concatenated_fasta, consensus_concatenated_gene_list, consensus_concatenated_dict, \
465 number_consensus_with_sequences = \
466 concatenate_extra_seq_2_consensus(consensus_files['noMatter'], reference_file, args.extraSeq,
467 rematch_second_outdir)
468 if len(consensus_concatenated_gene_list) > 0:
469 if args.mlst is None or \
470 (args.mlst is not None and number_consensus_with_sequences == len(gene_list_reference)):
471 time_taken_rematch_second, run_successfully_rematch_second, data_by_gene, \
472 sample_data_general_second, consensus_files, consensus_sequences = \
473 rematch_module.run_rematch_module(sample, fastq_files, consensus_concatenated_fasta,
474 args.threads, rematch_second_outdir, args.extraSeq,
475 args.minCovPresence, args.minCovCall,
476 args.minFrequencyDominantAllele, args.minGeneCoverage,
477 args.debug, args.numMapLoc,
478 args.minGeneIdentity, 'second',
479 args.softClip_baseQuality, args.softClip_recodeRun,
480 consensus_concatenated_dict,
481 args.softClip_cigarFlagRecode,
482 args.bowtieAlgo, args.bowtieOPT,
483 gene_list_reference, args.notWriteConsensus,
484 clean_run=True)
485 if not args.debug:
486 os.remove(consensus_concatenated_fasta)
487 if run_successfully_rematch_second:
488 if args.mlst is not None and (args.mlstRun == 'second' or args.mlstRun == 'all'):
489 run_get_st(sample, mlst_dicts, consensus_sequences, args.mlstConsensus, 'second',
490 workdir, time_str)
491 _ = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample, data_by_gene,
492 workdir, time_str, 'second_run', args.minGeneIdentity,
493 'coverage_depth', False, {})
494 if args.reportSequenceCoverage:
495 _ = write_data_by_gene(gene_list_reference, args.minGeneCoverage, sample,
496 data_by_gene, workdir, time_str, 'second_run',
497 args.minGeneIdentity, 'sequence_coverage', False, {})
498 else:
499 print('Some sequences missing after ReMatCh module first run. Second run will not be'
500 ' performed')
501 if os.path.isfile(consensus_concatenated_fasta):
502 os.remove(consensus_concatenated_fasta)
503 if os.path.isdir(rematch_second_outdir):
504 utils.remove_directory(rematch_second_outdir)
505 else:
506 print('No sequences left after ReMatCh module first run. Second run will not be performed')
507 if os.path.isfile(consensus_concatenated_fasta):
508 os.remove(consensus_concatenated_fasta)
509 if os.path.isdir(rematch_second_outdir):
510 utils.remove_directory(rematch_second_outdir)
511
512 if not searched_fastq_files and not args.keepDownloadedFastq and fastq_files is not None:
513 for fastq in fastq_files:
514 if os.path.isfile(fastq):
515 os.remove(fastq)
516
517 time_taken = utils.run_time(sample_start_time)
518
519 write_sample_report(sample, workdir, time_str, file_size, run_successfully_fastq,
520 run_successfully_rematch_first, run_successfully_rematch_second, time_taken_fastq,
521 time_taken_rematch_first, time_taken_rematch_second, time_taken, sequencing_information,
522 sample_data_general_first if run_successfully_rematch_first else
523 {'number_absent_genes': None, 'number_genes_multiple_alleles': None,
524 'mean_sample_coverage': None},
525 sample_data_general_second if run_successfully_rematch_second else
526 {'number_absent_genes': None, 'number_genes_multiple_alleles': None,
527 'mean_sample_coverage': None},
528 fastq_files if fastq_files is not None else '')
529
530 if all([run_successfully_fastq is not False,
531 run_successfully_rematch_first is not False,
532 run_successfully_rematch_second is not False]):
533 number_samples_successfully += 1
534
535 if args.summary:
536 write_summary_report(workdir, 'coverage_depth', time_str, gene_list_reference, genes_present_coverage_depth)
537 if args.reportSequenceCoverage:
538 write_summary_report(workdir, 'sequence_coverage', time_str, gene_list_reference,
539 genes_present_sequence_coverage)
540
541 return number_samples_successfully, len(list_ids)
542
543
544 def main():
545 if sys.version_info[0] < 3:
546 sys.exit('Must be using Python 3. Try calling "python3 rematch.py"')
547
548 parser = argparse.ArgumentParser(prog='rematch.py',
549 description='Reads mapping against target sequences, checking mapping and'
550 ' consensus sequences production',
551 formatter_class=argparse.ArgumentDefaultsHelpFormatter)
552 parser.add_argument('--version', help='Version information', action='version',
553 version='{prog} v{version}'.format(prog=parser.prog, version=__version__))
554
555 parser_optional_general = parser.add_argument_group('General facultative options')
556 parser_optional_general.add_argument('-r', '--reference', type=argparse.FileType('r'),
557 metavar='/path/to/reference_sequence.fasta',
558 help='Fasta file containing reference sequences', required=False)
559 parser_optional_general.add_argument('-w', '--workdir', type=str, metavar='/path/to/workdir/directory/',
560 help='Path to the directory where ReMatCh will run and produce the outputs'
561 ' with reads (ended with fastq.gz/fq.gz and, in case of PE data, pair-end'
562 ' direction coded as _R1_001 / _R2_001 or _1 / _2) already'
563 ' present (organized in sample folders) or to be downloaded',
564 required=False, default='.')
565 parser_optional_general.add_argument('-j', '--threads', type=int, metavar='N', help='Number of threads to use',
566 required=False, default=1)
567 parser_optional_general.add_argument('--mlst', type=str, metavar='"Streptococcus agalactiae"',
568 help='Species name (same as in PubMLST) to be used in MLST'
569 ' determination. ReMatCh will use Bowtie2 very-sensitive-local mapping'
570 ' parameters and will recode the soft clip CIGAR flags of the first run',
571 required=False)
572 parser_optional_general.add_argument('--doNotUseProvidedSoftware', action='store_true',
573 help='Tells ReMatCh to not use Bowtie2, Samtools and Bcftools that are'
574 ' provided with it')
575
576 parser_optional_download_exclusive = parser.add_mutually_exclusive_group()
577 parser_optional_download_exclusive.add_argument('-l', '--listIDs', type=argparse.FileType('r'),
578 metavar='/path/to/list_IDs.txt',
579 help='Path to list containing the IDs to be'
580 ' downloaded (one per line)', required=False)
581 parser_optional_download_exclusive.add_argument('-t', '--taxon', type=str, metavar='"Streptococcus agalactiae"',
582 help='Taxon name for which ReMatCh will download fastq files',
583 required=False)
584
585 parser_optional_rematch = parser.add_argument_group('ReMatCh module facultative options')
586 parser_optional_rematch.add_argument('--extraSeq', type=int, metavar='N',
587 help='Sequence length added to both ends of target sequences (usefull to'
588 ' improve reads mapping to the target one) that will be trimmed in'
589 ' ReMatCh outputs', required=False, default=0)
590 parser_optional_rematch.add_argument('--minCovPresence', type=int, metavar='N',
591 help='Reference position minimum coverage depth to consider the position to be'
592 ' present in the sample', required=False, default=5)
593 parser_optional_rematch.add_argument('--minCovCall', type=int, metavar='N',
594 help='Reference position minimum coverage depth to perform a base call. Lower'
595 ' coverage will be coded as N', required=False, default=10)
596 parser_optional_rematch.add_argument('--minFrequencyDominantAllele', type=float, metavar='0.6',
597 help='Minimum relative frequency of the dominant allele coverage depth (value'
598 ' between [0, 1]). Positions with lower values will be considered as'
599 ' having multiple alleles (and will be coded as N)', required=False,
600 default=0.6)
601 parser_optional_rematch.add_argument('--minGeneCoverage', type=int, metavar='N',
602 help='Minimum percentage of target reference gene sequence covered'
603 ' by --minCovPresence to consider a gene to be present (value'
604 ' between [0, 100])', required=False, default=70)
605 parser_optional_rematch.add_argument('--minGeneIdentity', type=int, metavar='N',
606 help='Minimum percentage of identity of reference gene sequence covered'
607 ' by --minCovCall to consider a gene to be present (value'
608 ' between [0, 100]). One INDEL will be considered as one difference',
609 required=False, default=80)
610 parser_optional_rematch.add_argument('--numMapLoc', type=int, metavar='N', help=argparse.SUPPRESS, required=False,
611 default=1)
612 # parser_optional_rematch.add_argument('--numMapLoc', type=int, metavar='N', help='Maximum number of locations to which a read can map (sometimes useful when mapping against similar sequences)', required=False, default=1)
613 parser_optional_rematch.add_argument('--doubleRun', action='store_true',
614 help='Tells ReMatCh to run a second time using as reference the noMatter'
615 ' consensus sequence produced in the first run. This will improve'
616 ' consensus sequence determination for sequences with high percentage of'
617 ' target reference gene sequence covered')
618 parser_optional_rematch.add_argument('--reportSequenceCoverage', action='store_true',
619 help='Produce an extra combined_report.data_by_gene with the sequence coverage'
620 ' instead of coverage depth')
621 parser_optional_rematch.add_argument('--summary', action='store_true',
622 help='Produce extra report files containing only sequences present in at least'
623 ' one sample (usefull when using a large number of reference'
624 ' sequences, and only for first run)')
625 parser_optional_rematch.add_argument('--notWriteConsensus', action='store_true',
626 help='Do not write consensus sequences')
627 parser_optional_rematch.add_argument('--bowtieAlgo', type=str, metavar='"--very-sensitive-local"',
628 help='Bowtie2 alignment mode. It can be an end-to-end alignment (unclipped'
629 ' alignment) or local alignment (soft clipped alignment). Also, can'
630 ' choose between fast or sensitive alignments. Please check Bowtie2'
631 ' manual for extra'
632 ' information: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml .'
633 ' This option should be provided between quotes and starting with'
634 ' an empty space (like --bowtieAlgo " --very-fast") or using equal'
635 ' sign (like --bowtieAlgo="--very-fast")',
636 required=False, default='--very-sensitive-local')
637 parser_optional_rematch.add_argument('--bowtieOPT', type=str, metavar='"--no-mixed"',
638 help='Extra Bowtie2 options. This option should be provided between quotes and'
639 ' starting with an empty space (like --bowtieOPT " --no-mixed") or using'
640 ' equal sign (like --bowtieOPT="--no-mixed")',
641 required=False)
642 parser_optional_rematch.add_argument('--debug', action='store_true',
643 help='DeBug Mode: do not remove temporary files')
644
645 parser_optional_mlst = parser.add_argument_group('MLST facultative options')
646 parser_optional_rematch.add_argument('--mlstReference', action='store_true',
647 help='If the curated scheme for MLST alleles is available, tells ReMatCh to'
648 ' use these as reference (force Bowtie2 to run with very-sensitive-local'
649 ' parameters, and sets --extraSeq to 200), otherwise ReMatCh uses the'
650 ' first alleles of each MLST gene fragment in PubMLST as reference'
651 ' sequences (force Bowtie2 to run with very-sensitive-local parameters,'
652 ' and sets --extraSeq to 0)')
653 parser_optional_mlst.add_argument('--mlstSchemaNumber', type=int, metavar='N',
654 help='Number of the species PubMLST schema to be used in case of multiple schemes'
655 ' available (by default will use the first schema)', required=False)
656 parser_optional_mlst.add_argument('--mlstConsensus', choices=['noMatter', 'correct', 'alignment', 'all'], type=str,
657 metavar='noMatter',
658 help='Consensus sequence to be used in MLST'
659 ' determination (available options: %(choices)s)', required=False,
660 default='noMatter')
661 parser_optional_mlst.add_argument('--mlstRun', choices=['first', 'second', 'all'], type=str, metavar='first',
662 help='ReMatCh run outputs to be used in MLST determination (available'
663 ' options: %(choices)s)', required=False, default='all')
664
665 parser_optional_download = parser.add_argument_group('Download facultative options')
666 parser_optional_download.add_argument('-a', '--asperaKey', type=argparse.FileType('r'),
667 metavar='/path/to/asperaweb_id_dsa.openssh',
668 help='Tells ReMatCh to download fastq files from ENA using Aspera'
669 ' Connect. With this option, the path to Private-key file'
670 ' asperaweb_id_dsa.openssh must be provided (normaly found in'
671 ' ~/.aspera/connect/etc/asperaweb_id_dsa.openssh).', required=False)
672 parser_optional_download.add_argument('-k', '--keepDownloadedFastq', action='store_true',
673 help='Tells ReMatCh to keep the fastq files downloaded')
674 parser_optional_download.add_argument('--downloadLibrariesType', type=str, metavar='PAIRED',
675 help='Tells ReMatCh to download files with specific library'
676 ' layout (available options: %(choices)s)',
677 choices=['PAIRED', 'SINGLE', 'BOTH'], required=False, default='BOTH')
678 parser_optional_download.add_argument('--downloadInstrumentPlatform', type=str, metavar='ILLUMINA',
679 help='Tells ReMatCh to download files with specific library layout (available'
680 ' options: %(choices)s)', choices=['ILLUMINA', 'ALL'], required=False,
681 default='ILLUMINA')
682 parser_optional_download.add_argument('--downloadCramBam', action='store_true',
683 help='Tells ReMatCh to also download cram/bam files and convert them to fastq'
684 ' files')
685
686 parser_optional_sra = parser.add_mutually_exclusive_group()
687 parser_optional_sra.add_argument('--SRA', action='store_true',
688 help='Tells getSeqENA.py to download reads in fastq format only from NCBI SRA'
689 ' database (not recommended)')
690 parser_optional_sra.add_argument('--SRAopt', action='store_true',
691 help='Tells getSeqENA.py to download reads from NCBI SRA if the download from ENA'
692 ' fails')
693
694 parser_optional_soft_clip = parser.add_argument_group('Soft clip facultative options')
695 parser_optional_soft_clip.add_argument('--softClip_baseQuality', type=int, metavar='N',
696 help='Base quality phred score in reads soft clipped regions',
697 required=False,
698 default=7)
699 parser_optional_soft_clip.add_argument('--softClip_recodeRun', type=str, metavar='first',
700 help='ReMatCh run to recode soft clipped regions (available'
701 ' options: %(choices)s)', choices=['first', 'second', 'both', 'none'],
702 required=False, default='none')
703 parser_optional_soft_clip.add_argument('--softClip_cigarFlagRecode', type=str, metavar='M',
704 help='CIGAR flag to recode CIGAR soft clip (available options: %(choices)s)',
705 choices=['M', 'I', 'X'], required=False, default='X')
706
707 args = parser.parse_args()
708
709 msg = []
710 if args.reference is None and not args.mlstReference:
711 msg.append('At least --reference or --mlstReference should be provided')
712 elif args.reference is not None and args.mlstReference:
713 msg.append('Only --reference or --mlstReference should be provided')
714 else:
715 if args.mlstReference:
716 if args.mlst is None:
717 msg.append('Please provide species name using --mlst')
718 if args.minFrequencyDominantAllele < 0 or args.minFrequencyDominantAllele > 1:
719 msg.append('--minFrequencyDominantAllele should be a value between [0, 1]')
720 if args.minGeneCoverage < 0 or args.minGeneCoverage > 100:
721 msg.append('--minGeneCoverage should be a value between [0, 100]')
722 if args.minGeneIdentity < 0 or args.minGeneIdentity > 100:
723 msg.append('--minGeneIdentity should be a value between [0, 100]')
724 if args.notWriteConsensus and args.doubleRun:
725 msg.append('--notWriteConsensus and --doubleRun cannot be used together.'
726 ' Maybe you only want to use --doubleRun')
727
728 if len(msg) > 0:
729 argparse.ArgumentParser.error('\n'.join(msg))
730
731 start_time = time.time()
732
733 number_samples_successfully, samples_total_number = run_rematch(args)
734
735 print('\n' + 'END ReMatCh')
736 print('\n' +
737 str(number_samples_successfully) + ' samples out of ' + str(samples_total_number) + ' run successfully')
738 time_taken = utils.run_time(start_time)
739 del time_taken
740
741 if number_samples_successfully == 0:
742 sys.exit('No samples run successfully!')
743
744
745 if __name__ == "__main__":
746 main()