Mercurial > repos > greg > gene_family_integrator

comparison gene_family_integrator.py @ 0:109a0eb7791f draft

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author greg
date Thu, 06 Apr 2017 13:34:02 -0400
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children f53cafa72117
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-1:000000000000 0:109a0eb7791f
1 #!/usr/bin/env python
2 import argparse
3 import subprocess
4
5 import utils.py
6
7 OUTPUT_DIR = 'integratedGeneFamilies_dir'
8
9 parser = argparse.ArgumentParser()
10 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
11 parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold')
12 parser.add_argument('--method', dest='method', help='Protein clustering method')
13 parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help='Use correspong coding sequences')
14 parser.add_argument('--output', dest='output', help="Output dataset")
15 parser.add_argument('--output_dir', dest='output_dir', help="Output dataset file_path directory")
16
17 args = parser.parse_args()
18
19 # Build the command line.
20 cmd = 'GeneFamilyIntegrator'
21 cmd += ' --orthogroup_faa %s' % args.orthogroup_fasta
22 cmd += ' --scaffold %s' % args.scaffold
23 cmd += ' --method %s' % args.method
24 if args.orthogroup_fna is not None:
25 cmd += ' --orthogroup_fna'
26 # Run the command.
27 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
28 rc = proc.wait()
29 utils.check_execution_errors(rc, proc.stderr)
30 utils.move_directory_files(OUTPUT_DIR, args.output_dir)
31 utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)