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Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
author trinity_ctat
date Thu, 12 Apr 2018 10:27:39 -0400
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45798c8f5b95 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
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1 #!/usr/bin/env python
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2
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3 import sys, subprocess, os
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4
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5 def stop_err( msg ):
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6 sys.stderr.write( "%s\n" % msg )
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7 sys.exit()
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8
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9 def __main__():
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10 # Get command-line arguments
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11 args = sys.argv
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12 # Remove name of calling program, i.e. ./stderr_wrapper.py
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13 args.pop(0)
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14
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15 # If there are no arguments left, we're done
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16 if len(args) == 0:
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17 return
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18
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19 # If one needs to silence stdout
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20 #args.append( ">" )
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21 #args.append( "/dev/null" )
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22
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23 cmdline = " ".join(args)
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26 try:
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27 # Run program
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28 err_capture = open("stderr.txt", 'w')
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29 proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout )
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30 returncode = proc.wait()
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31 err_capture.close()
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33
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34 if returncode != 0:
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35 raise Exception
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36
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37 except Exception:
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38 # Running Grinder failed: write error message to stderr
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39 err_text = open("stderr.txt").readlines()
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40 stop_err( "ERROR:\n" + "\n".join(err_text))
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43 if __name__ == "__main__": __main__()