deseq_and_sam2counts: deseq/stderr

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-:669899d20e59
+:a49aff09553e
+#!/usr/bin/python
+"""
+Wrapper that executes a program with its arguments but reports standard error
+messages only if the program exit status was not 0. This is useful to prevent
+Galaxy to interpret that there was an error if something was printed on stderr,
+e.g. if this was simply a warning.
+Example: ./stderr_wrapper.py myprog arg1 -f arg2
+Author: Florent Angly
+"""
+import sys, subprocess
+assert sys.version_info[:2] >= ( 2, 4 )
+def stop_err( msg ):
+sys.stderr.write( "%s\n" % msg )
+sys.exit()
+def __main__():
+# Get command-line arguments
+args = sys.argv
+# Remove name of calling program, i.e. ./stderr_wrapper.py
+args.pop(0)
+# If there are no arguments left, we're done
+if len(args) == 0:
+return
+# If one needs to silence stdout
+args.append( ">" )
+args.append( "/dev/null" )
+#cmdline = " ".join(args)
+#print cmdline
+try:
+# Run program
+proc = subprocess.Popen( args=args, shell=False, stderr=subprocess.PIPE )
+returncode = proc.wait()
+# Capture stderr, allowing for case where it's very large
+stderr = ''
+buffsize = 1048576
+try:
+while True:
+stderr += proc.stderr.read( buffsize )
+if not stderr or len( stderr ) % buffsize != 0:
+break
+except OverflowError:
+pass
+# Running Grinder failed: write error message to stderr
+if returncode != 0:
+raise Exception, stderr
+except Exception, e:
+# Running Grinder failed: write error message to stderr
+stop_err( 'Error: ' + str( e ) )
+if __name__ == "__main__": __main__()

Mercurial > repos > nikhil-joshi > deseq_and_sam2counts