Mercurial > repos > greg > plant_tribes_gene_family_phylogeny_builder
comparison gene_family_phylogeny_builder.py @ 0:7000422fbaff draft
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author | greg |
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date | Thu, 08 Jun 2017 12:51:58 -0400 |
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-1:000000000000 | 0:7000422fbaff |
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1 #!/usr/bin/env python | |
2 import argparse | |
3 import os | |
4 | |
5 import utils | |
6 | |
7 OUTPUT_DIR = 'geneFamilyPhylogenies_dir' | |
8 | |
9 parser = argparse.ArgumentParser() | |
10 | |
11 parser.add_argument('--alignment_type', dest='alignment_type', help='Input alignments type produced by the GeneFamilyAligner') | |
12 parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis') | |
13 parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files') | |
14 parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, help='Maximum number of sequences in orthogroup alignments') | |
15 parser.add_argument('--method', dest='method', help='Protein clustering method') | |
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') | |
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') | |
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', default=None, help='Output for phylogenetic trees') | |
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') | |
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') | |
26 parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method') | |
27 | |
28 args = parser.parse_args() | |
29 | |
30 # Build the command line. | |
31 cmd = 'GeneFamilyPhylogenyBuilder' | |
32 cmd += ' --alignment_type %s' % args.alignment_type | |
33 if args.bootstrap_replicates is not None: | |
34 cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates | |
35 cmd += ' --config_dir %s' % args.config_dir | |
36 cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size | |
37 cmd += ' --method %s' % args.method | |
38 cmd += ' --min_orthogroup_size %d' % args.min_orthogroup_size | |
39 cmd += ' --num_threads %d' % args.num_threads | |
40 cmd += ' --orthogroup_aln %s' % args.orthogroup_aln | |
41 if args.rooting_order is not None: | |
42 cmd += ' --rooting_order %s' % args.rooting_order | |
43 cmd += ' --scaffold %s' % args.scaffold | |
44 cmd += ' --sequence_type %s' % args.sequence_type | |
45 cmd += ' --tree_inference %s' % args.tree_inference | |
46 | |
47 # Run the command. | |
48 utils.run_command(cmd) | |
49 | |
50 # Handle outputs. | |
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') | |
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) | |
55 if args.output_tree is not None and args.output_tree_dir is not None: | |
56 src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree') | |
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) |