Mercurial > repos > gkumar09 > trinityrnaseq_protocol
comparison bash_command_executer.py @ 8:e40d92918044 draft
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author | gkumar09 |
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date | Wed, 23 Sep 2015 15:22:20 -0400 |
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7:a17bb21b711f | 8:e40d92918044 |
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1 #!/usr/bin/env python | |
2 | |
3 | |
4 import sys, subprocess, os | |
5 | |
6 def stop_err( msg ): | |
7 sys.stderr.write( "%s\n" % msg ) | |
8 sys.exit() | |
9 | |
10 def __main__(): | |
11 # Get command-line arguments | |
12 args = sys.argv | |
13 # Remove name of calling program, i.e. ./stderr_wrapper.py | |
14 args.pop(0) | |
15 | |
16 # If there are no arguments left, we're done | |
17 if len(args) == 0: | |
18 return | |
19 | |
20 # If one needs to silence stdout | |
21 #args.append( ">" ) | |
22 #args.append( "/dev/null" ) | |
23 | |
24 cmdline = " ".join(args) | |
25 | |
26 | |
27 try: | |
28 # Run program | |
29 err_capture = open("stderr.txt", 'w') | |
30 proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout ) | |
31 returncode = proc.wait() | |
32 err_capture.close() | |
33 | |
34 | |
35 if returncode != 0: | |
36 raise Exception | |
37 | |
38 except Exception: | |
39 # Running Grinder failed: write error message to stderr | |
40 err_text = open("stderr.txt").readlines() | |
41 stop_err( "ERROR:\n" + "\n".join(err_text)) | |
42 | |
43 | |
44 if __name__ == "__main__": __main__() |