Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.py @ 83:ed2cc7e78e9b draft

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author greg
date Fri, 13 Oct 2017 14:07:55 -0400
parents 03716365973d
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82:8378d126347a 83:ed2cc7e78e9b
18 parser.add_argument('--output_cleaned_cds', dest='output_cleaned_cds', help='Output transcripts.cleaned.cds') 18 parser.add_argument('--output_cleaned_cds', dest='output_cleaned_cds', help='Output transcripts.cleaned.cds')
19 parser.add_argument('--output_cleaned_nr_cds', dest='output_cleaned_nr_cds', default=None, help='Output transcripts.cleaned.nr.cds') 19 parser.add_argument('--output_cleaned_nr_cds', dest='output_cleaned_nr_cds', default=None, help='Output transcripts.cleaned.nr.cds')
20 parser.add_argument('--output_cleaned_nr_pep', dest='output_cleaned_nr_pep', default=None, help='Output transcripts.cleaned.nr.pep') 20 parser.add_argument('--output_cleaned_nr_pep', dest='output_cleaned_nr_pep', default=None, help='Output transcripts.cleaned.nr.pep')
21 parser.add_argument('--output_cleaned_pep', dest='output_cleaned_pep', help='Output transcripts.cleaned.pep') 21 parser.add_argument('--output_cleaned_pep', dest='output_cleaned_pep', help='Output transcripts.cleaned.pep')
22 parser.add_argument('--output_pep', dest='output_pep', help='Output transcripts.pep') 22 parser.add_argument('--output_pep', dest='output_pep', help='Output transcripts.pep')
23 parser.add_argument('--output_targeted_gene_families_stats', dest='output_targeted_gene_families_stats', default=None, help='Targeted gene families statistics')
23 parser.add_argument('--prediction_method', dest='prediction_method', help='Coding regions prediction method') 24 parser.add_argument('--prediction_method', dest='prediction_method', help='Coding regions prediction method')
24 parser.add_argument('--scaffold', dest='scaffold', default=None, help='Gene family scaffold') 25 parser.add_argument('--scaffold', dest='scaffold', default=None, help='Gene family scaffold')
25 parser.add_argument('--score_matrices', dest='score_matrices', default=None, help='Scores matrices') 26 parser.add_argument('--score_matrices', dest='score_matrices', default=None, help='Scores matrices')
26 parser.add_argument('--strand_specific', dest='strand_specific', default=None, help='Strand-specific assembly') 27 parser.add_argument('--strand_specific', dest='strand_specific', default=None, help='Strand-specific assembly')
27 parser.add_argument('--transcripts', dest='transcripts', help='Transcriptome assembly fasta file') 28 parser.add_argument('--transcripts', dest='transcripts', help='Transcriptome assembly fasta file')
59 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.cds'), args.output_cleaned_nr_cds) 60 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.cds'), args.output_cleaned_nr_cds)
60 if args.output_cleaned_nr_pep is not None: 61 if args.output_cleaned_nr_pep is not None:
61 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.pep'), args.output_cleaned_nr_pep) 62 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.pep'), args.output_cleaned_nr_pep)
62 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.pep'), args.output_cleaned_pep) 63 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.pep'), args.output_cleaned_pep)
63 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.pep'), args.output_pep) 64 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.pep'), args.output_pep)
65 if args.output_targeted_gene_families_stats is not None:
66 shutil.move(os.path.join(OUTPUT_DIR, 'targeted_gene_family_assemblies.stats'), args.output_targeted_gene_families_stats)