Mercurial > repos > greg > gene_family_integrator

comparison gene_family_integrator.py @ 6:1d178e90fbe6 draft

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author greg
date Mon, 10 Apr 2017 11:30:34 -0400
parents d06e3ae4eb5a
children 0bf47f620170
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5:077f036ca17d 6:1d178e90fbe6
6 6
7 OUTPUT_DIR = 'integratedGeneFamilies_dir' 7 OUTPUT_DIR = 'integratedGeneFamilies_dir'
8 8
9 parser = argparse.ArgumentParser() 9 parser = argparse.ArgumentParser()
10 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")
11 parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold') 11 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
12 parser.add_argument('--method', dest='method', help='Protein clustering method') 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') 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") 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") 15 parser.add_argument('--output_dir', dest='output_dir', help="Output dataset file_path directory")
16 16
25 cmd += ' --orthogroup_fna' 25 cmd += ' --orthogroup_fna'
26 # Run the command. 26 # Run the command.
27 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) 27 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
28 rc = proc.wait() 28 rc = proc.wait()
29 utils.check_execution_errors(rc, proc.stderr) 29 utils.check_execution_errors(rc, proc.stderr)
30 utils.move_directory_files(OUTPUT_DIR, args.output_dir) 30 utils.move_directory_files(os.path.join(OUTPUT_DIR, 'orthogroups_fasta'), args.output_dir)
31 utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir) 31 utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)