Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.py @ 19:f33369f4392a draft

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author greg
date Wed, 10 May 2017 14:29:26 -0400
parents 2f1de64cc3ae
children 451ad91530b8
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18:90a2e4ed5132 19:f33369f4392a
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import argparse 2 import argparse
3 import os
3 4
4 import utils 5 import utils
5 6
6 OUTPUT_DIR = 'phylogenomicsAnalysis_dir' 7 OUTPUT_DIR = 'geneFamilyPhylogenies_dir'
7 8
8 parser = argparse.ArgumentParser() 9 parser = argparse.ArgumentParser()
9 10
10 parser.add_argument('--alignment_type', dest='alignment_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')
11 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('--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')
14 parser.add_argument('--method', dest='method', help='Protein clustering method') 15 parser.add_argument('--method', dest='method', help='Protein clustering method')
15 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')
16 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')
17 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')
18 parser.add_argument('--output', dest='output', help='Output for phylogenetic trees') 19 parser.add_argument('--output_phylip', dest='output_phylip', default=None, help='Output for orthogroup phylip multiple sequence alignments')
19 parser.add_argument('--output_dir', dest='output_dir', help='output.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')
22 parser.add_argument('--output_tree_dir', dest='output_tree_dir', help='output_tree.files_path')
20 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')
21 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')
22 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')
23 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')
24 27
43 46
44 # Run the command. 47 # Run the command.
45 utils.run_command(cmd) 48 utils.run_command(cmd)
46 49
47 # Handle outputs. 50 # Handle outputs.
48 utils.move_directory_files(OUTPUT_DIR, args.output_dir) 51 if args.output_phylip is not None and args.output_phylip_dir is not None:
49 utils.write_html_output(args.output, 'Phylogenetic trees', args.output_dir) 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 src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree')
56 utils.move_directory_files(src_output_dir, args.output_tree_dir)
57 utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir)