Mercurial > repos > greg > gene_family_phylogeny_builder
comparison gene_family_phylogeny_builder.py @ 0:f4361d941aa3 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 11 Apr 2017 11:05:24 -0400 |
| parents | |
| children | f73151ec679b |
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| -1:000000000000 | 0:f4361d941aa3 |
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| 1 #!/usr/bin/env python | |
| 2 import argparse | |
| 3 import subprocess | |
| 4 | |
| 5 import utils | |
| 6 | |
| 7 OUTPUT_DIR = 'phylogenomicsAnalysis_dir' | |
| 8 | |
| 9 parser = argparse.ArgumentParser() | |
| 10 | |
| 11 parser.add_argument('--alignments_type', dest='alignments_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', dest='output', help='Output for phylogenetic trees') | |
| 20 parser.add_argument('--output_dir', dest='output_dir', help='output.files_path') | |
| 21 parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees') | |
| 22 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold') | |
| 23 parser.add_argument('--sequence_type', dest='sequence_type', help="Sequence type used in the phylogenetic inference") | |
| 24 parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method') | |
| 25 | |
| 26 args = parser.parse_args() | |
| 27 | |
| 28 # Build the command line. | |
| 29 cmd = 'GeneFamilyPhylogenyBuilder' | |
| 30 cmd += ' --alignment_type %s' % args.tree_inference | |
| 31 if args.bootstrap_replicates is not None: | |
| 32 cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates | |
| 33 cmd += ' --config_dir %s' % args.config_dir | |
| 34 cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size | |
| 35 cmd += ' --method %s' % args.method | |
| 36 cmd += ' --min_orthogroup_size %d' % args.min_orthogroup_size | |
| 37 cmd += ' --num_threads %d' % args.num_threads | |
| 38 cmd += ' --orthogroup_aln %s' % args.orthogroup_aln | |
| 39 if args.rooting_order is not None: | |
| 40 cmd += ' --rooting_order %s' % args.rooting_order | |
| 41 cmd += ' --scaffold %s' % args.scaffold | |
| 42 cmd += ' --sequence_type %s' % args.sequence_type | |
| 43 cmd += ' --tree_inference %s' % args.tree_inference | |
| 44 # Run the command. | |
| 45 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) | |
| 46 rc = proc.wait() | |
| 47 utils.check_execution_errors(rc, proc.stderr) | |
| 48 utils.move_directory_files(OUTPUT_DIR, args.output_dir) | |
| 49 utils.write_html_output(args.output, 'Phylogenetic trees', args.output_dir) |