Mercurial > repos > greg > plant_tribes_gene_family_phylogeny_builder
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gene_family_phylogeny_builder.py Thu Jun 08 12:51:58 2017 -0400 @@ -0,0 +1,58 @@ +#!/usr/bin/env python +import argparse +import os + +import utils + +OUTPUT_DIR = 'geneFamilyPhylogenies_dir' + +parser = argparse.ArgumentParser() + +parser.add_argument('--alignment_type', dest='alignment_type', help='Input alignments type produced by the GeneFamilyAligner') +parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis') +parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files') +parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, help='Maximum number of sequences in orthogroup alignments') +parser.add_argument('--method', dest='method', help='Protein clustering method') +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_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') +parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method') + +args = parser.parse_args() + +# Build the command line. +cmd = 'GeneFamilyPhylogenyBuilder' +cmd += ' --alignment_type %s' % args.alignment_type +if args.bootstrap_replicates is not None: + cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates +cmd += ' --config_dir %s' % args.config_dir +cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size +cmd += ' --method %s' % args.method +cmd += ' --min_orthogroup_size %d' % args.min_orthogroup_size +cmd += ' --num_threads %d' % args.num_threads +cmd += ' --orthogroup_aln %s' % args.orthogroup_aln +if args.rooting_order is not None: + cmd += ' --rooting_order %s' % args.rooting_order +cmd += ' --scaffold %s' % args.scaffold +cmd += ' --sequence_type %s' % args.sequence_type +cmd += ' --tree_inference %s' % args.tree_inference + +# Run the command. +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) +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)