Mercurial > repos > greg > gene_family_phylogeny_builder
changeset 24:61825c063bf3 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 12 May 2017 09:39:06 -0400 |
| parents | 4965a25fa094 |
| children | e6f16430822d |
| files | gene_family_phylogeny_builder.py |
| diffstat | 1 files changed, 5 insertions(+), 7 deletions(-) [+] |
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--- a/gene_family_phylogeny_builder.py Fri May 12 09:25:50 2017 -0400 +++ b/gene_family_phylogeny_builder.py Fri May 12 09:39:06 2017 -0400 @@ -16,8 +16,8 @@ parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, help='Minimum number of sequences in orthogroup alignments') parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') parser.add_argument('--orthogroup_aln', dest='orthogroup_aln', help='Input dataset files_path') -#parser.add_argument('--output_phylip', dest='output_phylip', default=None, help='Output for orthogroup phylip multiple sequence alignments') -#parser.add_argument('--output_phylip_dir', dest='output_phylip_dir', default=None, help='output_phylip.files_path') +parser.add_argument('--output_phylip', dest='output_phylip', default=None, help='Output for orthogroup phylip multiple sequence alignments') +parser.add_argument('--output_phylip_dir', dest='output_phylip_dir', default=None, help='output_phylip.files_path') #parser.add_argument('--output_tree', dest='output_tree', help='Output for phylogenetic trees') #parser.add_argument('--output_tree_dir', dest='output_tree_dir', help='output_tree.files_path') parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees') @@ -48,12 +48,10 @@ utils.run_command(cmd) # Handle outputs. -""" if args.output_phylip is not None and args.output_phylip_dir is not None: src_output_dir = os.path.join(OUTPUT_DIR, 'phylip_aln') utils.move_directory_files(src_output_dir, args.output_phylip_dir) utils.write_html_output(args.output_phylip, 'Orthogroup phylip multiple sequence alignments', args.output_phylip_dir) -src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree') -utils.move_directory_files(src_output_dir, args.output_tree_dir) -utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir) -""" +#src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree') +#utils.move_directory_files(src_output_dir, args.output_tree_dir) +#utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir)