Mercurial > repos > greg > meme_fimo

comparison fimo_wrapper.py @ 3:ce656b846c8e draft

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Uploaded
author greg
date Thu, 14 Apr 2016 11:22:23 -0400
parents 97fb2d36c482
children e85346ab5054
comparison
equal deleted inserted replaced
2:97fb2d36c482 3:ce656b846c8e
127 returncode = proc.wait() 127 returncode = proc.wait()
128 if returncode != 0: 128 if returncode != 0:
129 stderr = get_stderr(tmp_stderr) 129 stderr = get_stderr(tmp_stderr)
130 stop_err(stderr) 130 stop_err(stderr)
131 # Sort GFF output by a combination of chrom, score, start. 131 # Sort GFF output by a combination of chrom, score, start.
132 cmd = 'sort -k6,6n -k4,4n -k1,1 -o %s %s' % (gff_file, gff_file) 132 cmd = 'sort -k1,1 -k4,4n -k6,6n -o %s %s' % (gff_file, gff_file)
133 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True) 133 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True)
134 returncode = proc.wait() 134 returncode = proc.wait()
135 if returncode != 0: 135 if returncode != 0:
136 stderr = get_stderr(tmp_stderr) 136 stderr = get_stderr(tmp_stderr)
137 stop_err(stderr) 137 stop_err(stderr)