|
0
|
1 #!/usr/bin/env python
|
|
|
2 import argparse
|
|
|
3
|
|
|
4 import utils
|
|
|
5
|
|
|
6 OUTPUT_DIR = 'phylogenomicsAnalysis_dir'
|
|
|
7
|
|
|
8 parser = argparse.ArgumentParser()
|
|
|
9
|
|
5
|
10 parser.add_argument('--alignment_type', dest='alignment_type', help='Input alignments type produced by the GeneFamilyAligner')
|
|
0
|
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('--config_dir', dest='config_dir', help='Directory containing default configuration files')
|
|
|
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('--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('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
|
|
14
|
17 parser.add_argument('--orthogroup_aln', dest='orthogroup_aln', help='Input dataset files_path')
|
|
0
|
18 parser.add_argument('--output', dest='output', help='Output for phylogenetic trees')
|
|
|
19 parser.add_argument('--output_dir', dest='output_dir', help='output.files_path')
|
|
|
20 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')
|
|
14
|
22 parser.add_argument('--sequence_type', dest='sequence_type', help='Sequence type used in the phylogenetic inference')
|
|
0
|
23 parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method')
|
|
|
24
|
|
|
25 args = parser.parse_args()
|
|
|
26
|
|
|
27 # Build the command line.
|
|
|
28 cmd = 'GeneFamilyPhylogenyBuilder'
|
|
5
|
29 cmd += ' --alignment_type %s' % args.alignment_type
|
|
0
|
30 if args.bootstrap_replicates is not None:
|
|
|
31 cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates
|
|
|
32 cmd += ' --config_dir %s' % args.config_dir
|
|
|
33 cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size
|
|
|
34 cmd += ' --method %s' % args.method
|
|
|
35 cmd += ' --min_orthogroup_size %d' % args.min_orthogroup_size
|
|
|
36 cmd += ' --num_threads %d' % args.num_threads
|
|
|
37 cmd += ' --orthogroup_aln %s' % args.orthogroup_aln
|
|
|
38 if args.rooting_order is not None:
|
|
|
39 cmd += ' --rooting_order %s' % args.rooting_order
|
|
|
40 cmd += ' --scaffold %s' % args.scaffold
|
|
|
41 cmd += ' --sequence_type %s' % args.sequence_type
|
|
|
42 cmd += ' --tree_inference %s' % args.tree_inference
|
|
14
|
43
|
|
0
|
44 # Run the command.
|
|
14
|
45 utils.run_command(cmd)
|
|
|
46
|
|
|
47 # Handle outputs.
|
|
0
|
48 utils.move_directory_files(OUTPUT_DIR, args.output_dir)
|
|
|
49 utils.write_html_output(args.output, 'Phylogenetic trees', args.output_dir)
|
