Mercurial > repos > greg > plant_tribes_gene_family_integrator
view gene_family_integrator.py @ 2:a322e5e668a3 draft
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author | greg |
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date | Thu, 24 Aug 2017 13:32:01 -0400 |
parents | fa38de0b1f1a |
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#!/usr/bin/env python import argparse import os import utils OUTPUT_DIR = 'integratedGeneFamilies_dir' parser = argparse.ArgumentParser() parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets') parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold') parser.add_argument('--method', dest='method', help='Protein clustering method') parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help='Use correspong coding sequences') parser.add_argument('--output', dest='output', help='Output dataset') parser.add_argument('--output_dir', dest='output_dir', help='Output dataset file_path directory') args = parser.parse_args() # Build the command line. cmd = 'GeneFamilyIntegrator' cmd += ' --orthogroup_faa %s' % args.orthogroup_faa cmd += ' --scaffold %s' % args.scaffold cmd += ' --method %s' % args.method if args.orthogroup_fna is not None: cmd += ' --orthogroup_fna' # Run the command. utils.run_command(cmd) # Handle outputs. utils.move_directory_files(os.path.join(OUTPUT_DIR, 'orthogroups_fasta'), args.output_dir) utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)