Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.py @ 30:2de4563e70cf draft

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author greg
date Fri, 12 May 2017 14:14:27 -0400
parents 61825c063bf3
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29:3d78d366dfcc 30:2de4563e70cf
16 parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, help='Minimum number of sequences in orthogroup alignments') 16 parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, help='Minimum number of sequences in orthogroup alignments')
17 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') 17 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
18 parser.add_argument('--orthogroup_aln', dest='orthogroup_aln', help='Input dataset files_path') 18 parser.add_argument('--orthogroup_aln', dest='orthogroup_aln', help='Input dataset files_path')
19 parser.add_argument('--output_phylip', dest='output_phylip', default=None, help='Output for orthogroup phylip multiple sequence alignments') 19 parser.add_argument('--output_phylip', dest='output_phylip', default=None, help='Output for orthogroup phylip multiple sequence alignments')
20 parser.add_argument('--output_phylip_dir', dest='output_phylip_dir', default=None, help='output_phylip.files_path') 20 parser.add_argument('--output_phylip_dir', dest='output_phylip_dir', default=None, help='output_phylip.files_path')
21 #parser.add_argument('--output_tree', dest='output_tree', help='Output for phylogenetic trees') 21 parser.add_argument('--output_tree', dest='output_tree', default=None, help='Output for phylogenetic trees')
22 #parser.add_argument('--output_tree_dir', dest='output_tree_dir', help='output_tree.files_path') 22 parser.add_argument('--output_tree_dir', dest='output_tree_dir', default=None, help='output_tree.files_path')
23 parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees') 23 parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
24 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold') 24 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
25 parser.add_argument('--sequence_type', dest='sequence_type', help='Sequence type used in the phylogenetic inference') 25 parser.add_argument('--sequence_type', dest='sequence_type', help='Sequence type used in the phylogenetic inference')
26 parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method') 26 parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method')
27 27
50 # Handle outputs. 50 # Handle outputs.
51 if args.output_phylip is not None and args.output_phylip_dir is not None: 51 if args.output_phylip is not None and args.output_phylip_dir is not None:
52 src_output_dir = os.path.join(OUTPUT_DIR, 'phylip_aln') 52 src_output_dir = os.path.join(OUTPUT_DIR, 'phylip_aln')
53 utils.move_directory_files(src_output_dir, args.output_phylip_dir) 53 utils.move_directory_files(src_output_dir, args.output_phylip_dir)
54 utils.write_html_output(args.output_phylip, 'Orthogroup phylip multiple sequence alignments', args.output_phylip_dir) 54 utils.write_html_output(args.output_phylip, 'Orthogroup phylip multiple sequence alignments', args.output_phylip_dir)
55 #src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree') 55 if args.output_tree is not None and args.output_tree_dir is not None:
56 #utils.move_directory_files(src_output_dir, args.output_tree_dir) 56 src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree')
57 #utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir) 57 utils.move_directory_files(src_output_dir, args.output_tree_dir, copy=True)
58 utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir)