Mercurial > repos > greg > meme_fimo

comparison fimo_wrapper.py @ 2:97fb2d36c482 draft

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Uploaded
author greg
date Thu, 14 Apr 2016 11:18:57 -0400
parents a64feed0d508
children ce656b846c8e
comparison
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1:a64feed0d508 2:97fb2d36c482
117 shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output) 117 shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output)
118 118
119 gff_file = os.path.join(args.output_path, 'fimo.gff') 119 gff_file = os.path.join(args.output_path, 'fimo.gff')
120 if args.remove_duplicate_coords == 'yes': 120 if args.remove_duplicate_coords == 'yes':
121 tmp_stderr = tempfile.NamedTemporaryFile() 121 tmp_stderr = tempfile.NamedTemporaryFile()
122 # Sort GFF output by a combination of: score, start and coordinate. 122 # Identify and eliminating identical motif occurrences. These
123 # The output file is specified by -o FILE, and this operation is 123 # are identical if the combination of chrom, start, end and
124 # guaranteed safe (the file is read before being overwritten for output). 124 # motif id are identical.
125 cmd = 'sort -k6,6n -k4,4n -o %s %s' % (gff_file, gff_file) 125 cmd = 'sort -k1,1 -k4,4n -k5,5n -k9.1,9.6 -u -o %s %s' % (gff_file, gff_file)
126 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True) 126 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True)
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 by chromosome id, identifying and eliminating identical 131 # Sort GFF output by a combination of chrom, score, start.
132 # motif occurrences. 132 cmd = 'sort -k6,6n -k4,4n -k1,1 -o %s %s' % (gff_file, gff_file)
133 cmd = 'sort -k1,1 -o %s %s' % (gff_file, gff_file)
134 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True) 133 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True)
135 returncode = proc.wait() 134 returncode = proc.wait()
136 if returncode != 0: 135 if returncode != 0:
137 stderr = get_stderr(tmp_stderr) 136 stderr = get_stderr(tmp_stderr)
138 stop_err(stderr) 137 stop_err(stderr)