Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.py @ 3:962feb5f0818 draft

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Uploaded
author greg
date Fri, 07 Apr 2017 13:46:39 -0400
parents 01c08c35d051
children 3f75c91767f9
comparison
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2:01c08c35d051 3:962feb5f0818
48 cmd += ' --iterative_realignment %d' % args.iterative_realignment 48 cmd += ' --iterative_realignment %d' % args.iterative_realignment
49 # Run the command. 49 # Run the command.
50 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) 50 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
51 rc = proc.wait() 51 rc = proc.wait()
52 utils.check_execution_errors(rc, proc.stderr) 52 utils.check_execution_errors(rc, proc.stderr)
53 utils.move_directory_files(OUTPUT_DIR, args.output_dir) 53 if args.codon_alignments is None:
54 src_output_dir = OUTPUT_DIR
55 else:
56 src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln')
57 utils.move_directory_files(src_output_dir, args.output_dir)
54 utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir) 58 utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir)