Mercurial > repos > computational-metabolomics > sirius_csifingerid

comparison sirius_csifingerid.py @ 4:8fb51147d15e draft

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"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388"
author computational-metabolomics
date Fri, 04 Feb 2022 10:09:40 +0000
parents 4cbfd3d0a4c4
children 96b077221201
comparison
equal deleted inserted replaced
3:4cbfd3d0a4c4 4:8fb51147d15e
388 reader = csv.DictReader(infile, delimiter='\t') 388 reader = csv.DictReader(infile, delimiter='\t')
389 389
390 ad = paramds[fn.split(os.sep)[-2]]['additional_details'] 390 ad = paramds[fn.split(os.sep)[-2]]['additional_details']
391 391
392 for line in reader: 392 for line in reader:
393 if 'rank' in line and \ 393 if 'rank' in line \
394 0 < int(rank_filter) < int(line['rank']): 394 and 0 < int(rank_filter) < int(line['rank']):
395 # filter out those annotations greater than rank filter 395 # filter out those annotations greater than rank filter
396 # If rank_filter is zero then skip 396 # If rank_filter is zero then skip
397 continue 397 continue
398 398
399 if 'ConfidenceScore' in line \ 399 if ('ConfidenceScore' in line
400 and 0 < int(confidence_filter) < int(line['rank']): 400 and 0 < float(confidence_filter)
401 # filter out those annotations greater than rank filter 401 and float(line['ConfidenceScore']) <
402 # If rank_filter is zero then skip 402 float(confidence_filter)):
403 # filter out those annotations that are less than
404 # the confidence filter value
403 continue 405 continue
404 line.update(ad) 406 line.update(ad)
405 407
406 dwriter.writerow(line) 408 dwriter.writerow(line)
407 409
412 os.system(s1) 414 os.system(s1)
413 s2 = "sed 's/CSI:FingerIDScore/Score/' {r} > {r}".format(r=result_pth) 415 s2 = "sed 's/CSI:FingerIDScore/Score/' {r} > {r}".format(r=result_pth)
414 os.system(s2) 416 os.system(s2)
415 417
416 418
417 concat_output('canopus_summary.tsv', 419 concat_output('compound_identifications.tsv',
418 args.canopus_result_pth, 420 args.annotations_result_pth,
419 args.rank_filter, 421 args.rank_filter,
420 args.confidence_filter, 422 args.confidence_filter,
421 args.backwards_compatible) 423 args.backwards_compatible)
422 concat_output('compound_identifications.tsv', 424 concat_output('canopus_summary.tsv',
423 args.annotations_result_pth, 425 args.canopus_result_pth,
424 0, 426 0,
425 0, 427 0,
426 False) 428 False)