Mercurial > repos > greg > assembly_post_processor
comparison assembly_post_processor.py @ 74:9da5dc4b99cc draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 05 Oct 2017 13:54:37 -0400 |
| parents | baf10f7f3d4a |
| children | 37ed984d934e |
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| 73:b472981ad5c5 | 74:9da5dc4b99cc |
|---|---|
| 11 parser.add_argument('--dereplicate', dest='dereplicate', default=None, help='Remove duplicate sequences') | 11 parser.add_argument('--dereplicate', dest='dereplicate', default=None, help='Remove duplicate sequences') |
| 12 parser.add_argument('--gap_trimming', dest='gap_trimming', type=float, default=0, help='Trim alignments') | 12 parser.add_argument('--gap_trimming', dest='gap_trimming', type=float, default=0, help='Trim alignments') |
| 13 parser.add_argument('--gene_family_search', dest='gene_family_search', default=None, help='Targeted gene families') | 13 parser.add_argument('--gene_family_search', dest='gene_family_search', default=None, help='Targeted gene families') |
| 14 parser.add_argument('--method', dest='method', default=None, help='Protein clustering method') | 14 parser.add_argument('--method', dest='method', default=None, help='Protein clustering method') |
| 15 parser.add_argument('--min_length', dest='min_length', type=int, default=0, help='Minimum sequence length') | 15 parser.add_argument('--min_length', dest='min_length', type=int, default=0, help='Minimum sequence length') |
| 16 parser.add_argument('--move_stats', dest='move_stats', default=None, help='Flag to move primary targeted gene families statistics datasets') | |
| 16 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of processors') | 17 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of processors') |
| 17 parser.add_argument('--output_pttgf', dest='output_pttgf', default=None, help='Primary targeted gene families dataset') | |
| 18 parser.add_argument('--output_cds', dest='output_cds', help='Output transcripts.cds') | 18 parser.add_argument('--output_cds', dest='output_cds', help='Output transcripts.cds') |
| 19 parser.add_argument('--output_cleaned_cds', dest='output_cleaned_cds', help='Output transcripts.cleaned.cds') | 19 parser.add_argument('--output_cleaned_cds', dest='output_cleaned_cds', help='Output transcripts.cleaned.cds') |
| 20 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_cds', dest='output_cleaned_nr_cds', default=None, help='Output transcripts.cleaned.nr.cds') |
| 21 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_nr_pep', dest='output_cleaned_nr_pep', default=None, help='Output transcripts.cleaned.nr.pep') |
| 22 parser.add_argument('--output_cleaned_pep', dest='output_cleaned_pep', help='Output transcripts.cleaned.pep') | 22 parser.add_argument('--output_cleaned_pep', dest='output_cleaned_pep', help='Output transcripts.cleaned.pep') |
| 23 parser.add_argument('--output_pep', dest='output_pep', help='Output transcripts.pep') | 23 parser.add_argument('--output_pep', dest='output_pep', help='Output transcripts.pep') |
| 24 parser.add_argument('--output_pttgf_dir', dest='output_pttgf_dir', default=None, help='Directory hierarchy of targeted gene family datasets') | |
| 25 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') |
| 26 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') |
| 27 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') |
| 28 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') |
| 29 parser.add_argument('--transcripts', dest='transcripts', help='Transcriptome assembly fasta file') | 28 parser.add_argument('--transcripts', dest='transcripts', help='Transcriptome assembly fasta file') |
| 61 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) |
| 62 if args.output_cleaned_nr_pep is not None: | 61 if args.output_cleaned_nr_pep is not None: |
| 63 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) |
| 64 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) |
| 65 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) |
| 66 if args.output_pttgf is not None and args.output_pttgf_dir is not None: | 65 if args.move_stats is not None: |
| 67 src_output_dir = os.path.join(OUTPUT_DIR, 'targeted_gene_families') | 66 src_dir = os.path.join(OUTPUT_DIR, 'targeted_gene_families') |
| 68 utils.move_directory_files(src_output_dir, args.output_pttgf_dir) | 67 dst_dir = os.path.join(OUTPUT_DIR, 'targeted_gene_families_statistics') |
| 69 utils.write_html_output(args.output_pttgf, 'Targeted gene families', args.output_pttgf_dir) | 68 shutil.move(os.path.join(src_dir, '*.stats'), dst_dir) |