Mercurial > repos > jjohnson > mzsqlite_psm_align
comparison mzsqlite_psm_align.py @ 5:af5f22779a8e draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
| author | jjohnson |
|---|---|
| date | Tue, 10 Apr 2018 11:52:04 -0400 |
| parents | 492f98d89e26 |
| children |
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| 4:a96b2754171c | 5:af5f22779a8e |
|---|---|
| 407 help='Genome reference sequence in 2bit format') | 407 help='Genome reference sequence in 2bit format') |
| 408 parser.add_argument( | 408 parser.add_argument( |
| 409 '-r', '--reads_bam', default=None, | 409 '-r', '--reads_bam', default=None, |
| 410 help='reads alignment bam path') | 410 help='reads alignment bam path') |
| 411 parser.add_argument( | 411 parser.add_argument( |
| 412 '-g', '--gffutils_file', default=None, | 412 '-g', '--gffutils_sqlite', default=None, |
| 413 help='gffutils GTF sqlite DB') | 413 help='gffutils GTF sqlite DB') |
| 414 parser.add_argument( | 414 parser.add_argument( |
| 415 '-B', '--probed', default=None, | 415 '-B', '--probed', default=None, |
| 416 help='proBed path') | 416 help='proBed path') |
| 417 parser.add_argument( | 417 parser.add_argument( |
| 441 samfile = pysam.AlignmentFile(args.reads_bam, "rb" ) if args.reads_bam else None | 441 samfile = pysam.AlignmentFile(args.reads_bam, "rb" ) if args.reads_bam else None |
| 442 seqlens = twobit.sequence_sizes() | 442 seqlens = twobit.sequence_sizes() |
| 443 | 443 |
| 444 probed = open(args.probed,'w') if args.probed else sys.stdout | 444 probed = open(args.probed,'w') if args.probed else sys.stdout |
| 445 | 445 |
| 446 gff_cursor = get_connection(args.gffutils_file).cursor() if args.gffutils_file else None | 446 gff_cursor = get_connection(args.gffutils_sqlite).cursor() if args.gffutils_sqlite else None |
| 447 map_cursor = get_connection(args.genomic_mapping_sqlite).cursor() | 447 map_cursor = get_connection(args.genomic_mapping_sqlite).cursor() |
| 448 mz_cursor = get_connection(args.mzsqlite_file).cursor() | 448 mz_cursor = get_connection(args.mzsqlite).cursor() |
| 449 | 449 |
| 450 unmapped_accs = set() | 450 unmapped_accs = set() |
| 451 timings = dict() | 451 timings = dict() |
| 452 def add_time(name,elapsed): | 452 def add_time(name,elapsed): |
| 453 if name in timings: | 453 if name in timings: |
| 654 locations.add('%s:%s-%s:%s' % (start_chrom,start_pos,end_chrom,end_pos)) | 654 locations.add('%s:%s-%s:%s' % (start_chrom,start_pos,end_chrom,end_pos)) |
| 655 te = time() | 655 te = time() |
| 656 add_time('GENOMIC_POS_QUERY',te - ts) | 656 add_time('GENOMIC_POS_QUERY',te - ts) |
| 657 except: | 657 except: |
| 658 unmapped_accs.add(acc) | 658 unmapped_accs.add(acc) |
| 659 print('Unmapped: %s' % acc, file=sys.stderr) | 659 if args.debug: |
| 660 print('Unmapped: %s' % acc, file=sys.stderr) | |
| 660 return len(locations) | 661 return len(locations) |
| 661 return -1 | 662 return -1 |
| 662 | 663 |
| 663 def spectrum_peptide_count(spectrum_id): | 664 def spectrum_peptide_count(spectrum_id): |
| 664 ts = time() | 665 ts = time() |
| 727 for i in range(3): | 728 for i in range(3): |
| 728 if i < ao: | 729 if i < ao: |
| 729 bases.append(list(set([c[i] for c in aa_codon_map[aa]]))) | 730 bases.append(list(set([c[i] for c in aa_codon_map[aa]]))) |
| 730 else: | 731 else: |
| 731 bases.append([b for b, cnt in reversed(sorted(pileup[idx + i]['bases'].iteritems(), key=lambda (k,v): (v,k)))]) | 732 bases.append([b for b, cnt in reversed(sorted(pileup[idx + i]['bases'].iteritems(), key=lambda (k,v): (v,k)))]) |
| 732 print('%s' % bases) | 733 if args.debug: |
| 734 print('%s' % bases,file=sys.stderr) | |
| 733 for b0 in bases[0]: | 735 for b0 in bases[0]: |
| 734 if b0 not in aa_na_map[aa]: | 736 if b0 not in aa_na_map[aa]: |
| 735 continue | 737 continue |
| 736 for b1 in bases[1]: | 738 for b1 in bases[1]: |
| 737 if b1 not in aa_na_map[aa][b0]: | 739 if b1 not in aa_na_map[aa][b0]: |
| 810 'XT' : 'i', #Enzyme specificity | 812 'XT' : 'i', #Enzyme specificity |
| 811 'XE' : 'i', #Enzyme used in the experiment | 813 'XE' : 'i', #Enzyme used in the experiment |
| 812 'XG' : 'A', #Peptide type | 814 'XG' : 'A', #Peptide type |
| 813 'XU' : 'Z', #URI | 815 'XU' : 'Z', #URI |
| 814 """ | 816 """ |
| 815 psm_cursor = get_connection(args.mzsqlite_file).cursor() | 817 psm_cursor = get_connection(args.mzsqlite).cursor() |
| 816 ts = time() | 818 ts = time() |
| 817 psms = psm_cursor.execute(PSM_QUERY) | 819 psms = psm_cursor.execute(PSM_QUERY) |
| 818 te = time() | 820 te = time() |
| 819 add_time('PSM_QUERY',te - ts) | 821 add_time('PSM_QUERY',te - ts) |
| 820 proBAM = ProBAM(species=None,assembly=args.genomeReference,seqlens=seqlens,comments=[]) | 822 proBAM = ProBAM(species=None,assembly=args.genomeReference,seqlens=seqlens,comments=[]) |