Mercurial > repos > greg > gene_family_integrator

comparison gene_family_integrator.py @ 13:49bdc3b38b4a draft

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author greg
date Fri, 05 May 2017 09:33:06 -0400
parents 0bf47f620170
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12:57f27f72c771 13:49bdc3b38b4a
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import argparse 2 import argparse
3 import os 3 import os
4 import subprocess
5 4
6 import utils 5 import utils
7 6
8 OUTPUT_DIR = 'integratedGeneFamilies_dir' 7 OUTPUT_DIR = 'integratedGeneFamilies_dir'
9 8
10 parser = argparse.ArgumentParser() 9 parser = argparse.ArgumentParser()
11 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets") 10 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets')
12 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold') 11 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
13 parser.add_argument('--method', dest='method', help='Protein clustering method') 12 parser.add_argument('--method', dest='method', help='Protein clustering method')
14 parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help='Use correspong coding sequences') 13 parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help='Use correspong coding sequences')
15 parser.add_argument('--output', dest='output', help="Output dataset") 14 parser.add_argument('--output', dest='output', help='Output dataset')
16 parser.add_argument('--output_dir', dest='output_dir', help="Output dataset file_path directory") 15 parser.add_argument('--output_dir', dest='output_dir', help='Output dataset file_path directory')
17 16
18 args = parser.parse_args() 17 args = parser.parse_args()
19 18
20 # Build the command line. 19 # Build the command line.
21 cmd = 'GeneFamilyIntegrator' 20 cmd = 'GeneFamilyIntegrator'
22 cmd += ' --orthogroup_faa %s' % args.orthogroup_faa 21 cmd += ' --orthogroup_faa %s' % args.orthogroup_faa
23 cmd += ' --scaffold %s' % args.scaffold 22 cmd += ' --scaffold %s' % args.scaffold
24 cmd += ' --method %s' % args.method 23 cmd += ' --method %s' % args.method
25 if args.orthogroup_fna is not None: 24 if args.orthogroup_fna is not None:
26 cmd += ' --orthogroup_fna' 25 cmd += ' --orthogroup_fna'
26
27 # Run the command. 27 # Run the command.
28 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) 28 utils.run_command(cmd)
29 rc = proc.wait() 29
30 utils.check_execution_errors(rc, proc.stderr) 30 # Handle outputs.
31 utils.move_directory_files(os.path.join(OUTPUT_DIR, 'orthogroups_fasta'), args.output_dir) 31 utils.move_directory_files(os.path.join(OUTPUT_DIR, 'orthogroups_fasta'), args.output_dir)
32 utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir) 32 utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)