Mercurial > repos > greg > plant_tribes_gene_family_aligner
changeset 1:ab1f0bab96f3 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 01 Aug 2017 14:25:14 -0400 |
| parents | 7ba9469800b9 |
| children | 2810338344a1 |
| files | gene_family_aligner.py |
| diffstat | 1 files changed, 3 insertions(+), 0 deletions(-) [+] |
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--- a/gene_family_aligner.py Thu Jun 08 12:46:20 2017 -0400 +++ b/gene_family_aligner.py Tue Aug 01 14:25:14 2017 -0400 @@ -16,6 +16,7 @@ parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets') parser.add_argument('--output', dest='output', help='Output dataset') parser.add_argument('--output_dir', dest='output_dir', help='Output dataset files_path directory') +parser.add_argument('--output_dataset_collection', dest='output_dataset_collection', default=None, help='Output additional dataset collection of files.') parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='Maximum number of iteration that the PASTA algorithm will execute') parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta') parser.add_argument('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of') @@ -51,5 +52,7 @@ src_output_dir = OUTPUT_DIR else: src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln') +if args.output_dataset_collection is not None: + utils.move_directory_files(src_output_dir, args.output_dataset_collection, copy=True) utils.move_directory_files(src_output_dir, args.output_dir) utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir)