Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.py @ 49:9d58af3e459d draft

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Uploaded
author greg
date Fri, 05 May 2017 09:30:34 -0400
parents b7858b1f64f1
children 9a105e8f08e5
comparison
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48:564163c7afd8 49:9d58af3e459d
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import argparse 2 import argparse
3 import os
4 import subprocess
5 3
6 import utils 4 import utils
7
8 OUTPUT_DIR = 'assemblyPostProcessor_dir'
9 5
10 parser = argparse.ArgumentParser() 6 parser = argparse.ArgumentParser()
11 parser.add_argument('--dereplicate', dest='dereplicate', default=None, help='Remove duplicate sequences') 7 parser.add_argument('--dereplicate', dest='dereplicate', default=None, help='Remove duplicate sequences')
12 parser.add_argument('--gap_trimming', dest='gap_trimming', type=float, default=0, help='Trim alignments') 8 parser.add_argument('--gap_trimming', dest='gap_trimming', type=float, default=0, help='Trim alignments')
13 parser.add_argument('--gene_family_search', dest='gene_family_search', default=None, help='Targeted gene families') 9 parser.add_argument('--gene_family_search', dest='gene_family_search', default=None, help='Targeted gene families')
41 if args.score_matrices is not None: 37 if args.score_matrices is not None:
42 cmd += ' --score_matrices %s' % args.score_matrices 38 cmd += ' --score_matrices %s' % args.score_matrices
43 if args.strand_specific is not None: 39 if args.strand_specific is not None:
44 cmd += ' --strand_specific' 40 cmd += ' --strand_specific'
45 cmd += ' --transcripts %s' % args.transcripts 41 cmd += ' --transcripts %s' % args.transcripts
46
47 # Run the command. 42 # Run the command.
48 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) 43 utils.run_command(cmd)
49 rc = proc.wait()
50 utils.check_execution_errors(rc, proc.stderr, proc.stdout)