Mercurial > repos > gkumar09 > trinityrnaseq_protocol
comparison bash_command_executer.py @ 8:e40d92918044 draft
Uploaded
| author | gkumar09 |
|---|---|
| date | Wed, 23 Sep 2015 15:22:20 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 7:a17bb21b711f | 8:e40d92918044 |
|---|---|
| 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__() |
