Mercurial > repos > iuc > meme_fimo

comparison fimo_wrapper.py @ 11:c470b36b592d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
author iuc
date Wed, 23 Aug 2017 20:57:21 -0400
parents 40b8472e91ca
children
comparison
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10:307b2f3559bf 11:c470b36b592d
110 proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr) 110 proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr)
111 returncode = proc.wait() 111 returncode = proc.wait()
112 if returncode != 0: 112 if returncode != 0:
113 stderr = get_stderr(tmp_stderr) 113 stderr = get_stderr(tmp_stderr)
114 stop_err(stderr) 114 stop_err(stderr)
115 except Exception, e: 115 except Exception as e:
116 stop_err('Error running FIMO:\n%s' % str(e)) 116 stop_err('Error running FIMO:\n%s' % e)
117 117
118 shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output) 118 shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output)
119 119
120 gff_file = os.path.join(args.output_path, 'fimo.gff') 120 gff_file = os.path.join(args.output_path, 'fimo.gff')
121 if args.remove_duplicate_coords == 'yes': 121 if args.remove_duplicate_coords == 'yes':