Mercurial > repos > trinity_ctat > ctat_concatenate
comparison ctat_bash_command_executer.py @ 0:702a3586942a draft default tip
Upload ctat tools.
| author | trinity_ctat |
|---|---|
| date | Tue, 17 Jul 2018 11:48:23 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:702a3586942a |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 import sys, subprocess, os | |
| 4 | |
| 5 def stop_err( msg ): | |
| 6 sys.stderr.write( "%s\n" % msg ) | |
| 7 sys.exit() | |
| 8 | |
| 9 def __main__(): | |
| 10 # Get command-line arguments | |
| 11 args = sys.argv | |
| 12 # Remove name of calling program, i.e. ./stderr_wrapper.py | |
| 13 args.pop(0) | |
| 14 | |
| 15 # If there are no arguments left, we're done | |
| 16 if len(args) == 0: | |
| 17 return | |
| 18 | |
| 19 # If one needs to silence stdout | |
| 20 #args.append( ">" ) | |
| 21 #args.append( "/dev/null" ) | |
| 22 | |
| 23 cmdline = " ".join(args) | |
| 24 | |
| 25 | |
| 26 try: | |
| 27 # Run program | |
| 28 err_capture = open("stderr.txt", 'w') | |
| 29 proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout ) | |
| 30 returncode = proc.wait() | |
| 31 err_capture.close() | |
| 32 | |
| 33 | |
| 34 if returncode != 0: | |
| 35 raise Exception | |
| 36 | |
| 37 except Exception: | |
| 38 # Running Grinder failed: write error message to stderr | |
| 39 err_text = open("stderr.txt").readlines() | |
| 40 stop_err( "ERROR:\n" + "\n".join(err_text)) | |
| 41 | |
| 42 | |
| 43 if __name__ == "__main__": __main__() |