Mercurial > repos > greg > gene_family_phylogeny_builder
changeset 30:2de4563e70cf draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 12 May 2017 14:14:27 -0400 |
| parents | 3d78d366dfcc |
| children | a456fb4d1d44 |
| files | gene_family_phylogeny_builder.py |
| diffstat | 1 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/gene_family_phylogeny_builder.py Fri May 12 14:14:19 2017 -0400 +++ b/gene_family_phylogeny_builder.py Fri May 12 14:14:27 2017 -0400 @@ -18,8 +18,8 @@ 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_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('--output_tree', dest='output_tree', default=None, help='Output for phylogenetic trees') +parser.add_argument('--output_tree_dir', dest='output_tree_dir', default=None, help='output_tree.files_path') parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees') parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold') parser.add_argument('--sequence_type', dest='sequence_type', help='Sequence type used in the phylogenetic inference') @@ -52,6 +52,7 @@ 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) +if args.output_tree is not None and args.output_tree_dir is not None: + src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree') + utils.move_directory_files(src_output_dir, args.output_tree_dir, copy=True) + utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir)