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Added wrapper script for correct stderr handling
author geert-vandeweyer
date Thu, 10 Apr 2014 09:44:09 -0400
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1:3182c7fac413 2:14567aa2be12
1 #!/usr/bin/env python
2
3 """
4 Wrapper that execute a program and its arguments but reports standard error
5 messages only if the program exit status was not 0
6 Example: ./stderr_wrapper.py myprog arg1 -f arg2
7
8 Taken from bcftools_view package of gregory-minevich
9 """
10
11 import sys, subprocess
12
13 assert sys.version_info[:2] >= ( 2, 4 )
14
15 def stop_err( msg ):
16 sys.stderr.write( "%s\n" % msg )
17 sys.exit()
18
19 def __main__():
20 # Get command-line arguments
21 args = sys.argv
22 # Remove name of calling program, i.e. ./stderr_wrapper.py
23 args.pop(0)
24 # If there are no arguments left, we're done
25 if len(args) == 0:
26 return
27
28 # If one needs to silence stdout
29 #args.append( ">" )
30 #args.append( "/dev/null" )
31
32 cmdline = " ".join(args)
33 try:
34 # Run program
35 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
36 returncode = proc.wait()
37 # Capture stderr, allowing for case where it's very large
38 stderr = ''
39 buffsize = 1048576
40 try:
41 while True:
42 stderr += proc.stderr.read( buffsize )
43 if not stderr or len( stderr ) % buffsize != 0:
44 break
45 except OverflowError:
46 pass
47 # Running BCFtools failed: write error message to stderr
48 if returncode != 0:
49 raise Exception, stderr
50 except Exception, e:
51 # Running BCFtools failed: write error message to stderr
52 stop_err( 'Error:\n' + str( e ) )
53
54
55 if __name__ == "__main__": __main__()