Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.py @ 5:f73151ec679b draft

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author greg
date Tue, 11 Apr 2017 13:18:16 -0400
parents f4361d941aa3
children 2f1de64cc3ae
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4:b78f5b0d0805 5:f73151ec679b
6 6
7 OUTPUT_DIR = 'phylogenomicsAnalysis_dir' 7 OUTPUT_DIR = 'phylogenomicsAnalysis_dir'
8 8
9 parser = argparse.ArgumentParser() 9 parser = argparse.ArgumentParser()
10 10
11 parser.add_argument('--alignments_type', dest='alignments_type', help='Input alignments type produced by the GeneFamilyAligner') 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') 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') 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') 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') 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') 16 parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, help='Minimum number of sequences in orthogroup alignments')
25 25
26 args = parser.parse_args() 26 args = parser.parse_args()
27 27
28 # Build the command line. 28 # Build the command line.
29 cmd = 'GeneFamilyPhylogenyBuilder' 29 cmd = 'GeneFamilyPhylogenyBuilder'
30 cmd += ' --alignment_type %s' % args.tree_inference 30 cmd += ' --alignment_type %s' % args.alignment_type
31 if args.bootstrap_replicates is not None: 31 if args.bootstrap_replicates is not None:
32 cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates 32 cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates
33 cmd += ' --config_dir %s' % args.config_dir 33 cmd += ' --config_dir %s' % args.config_dir
34 cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size 34 cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size
35 cmd += ' --method %s' % args.method 35 cmd += ' --method %s' % args.method