Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4_make_bam.py @ 31:fd95aaef8818 draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c
author peterjc
date Wed, 10 Feb 2016 09:07:39 -0500
parents 55ae131c5862
children 56b421d59805
comparison
equal deleted inserted replaced
30:b506e3b779fa 31:fd95aaef8818
4 import os 4 import os
5 import sys 5 import sys
6 import shutil 6 import shutil
7 import subprocess 7 import subprocess
8 import tempfile 8 import tempfile
9
10 def sys_exit(msg, err=1):
11 sys.stderr.write(msg+"\n")
12 sys.exit(err)
13 9
14 def run(cmd, log_handle): 10 def run(cmd, log_handle):
15 try: 11 try:
16 child = subprocess.Popen(cmd, shell=True, 12 child = subprocess.Popen(cmd, shell=True,
17 stdout=subprocess.PIPE, 13 stdout=subprocess.PIPE,
87 83
88 if __name__ == "__main__": 84 if __name__ == "__main__":
89 mira_convert, maf_file, fasta_file, bam_file = sys.argv[1:] 85 mira_convert, maf_file, fasta_file, bam_file = sys.argv[1:]
90 msg = make_bam(mira_convert, maf_file, fasta_file, bam_file, sys.stdout) 86 msg = make_bam(mira_convert, maf_file, fasta_file, bam_file, sys.stdout)
91 if msg: 87 if msg:
92 sys_exit(msg) 88 sys.exit(msg)