Mercurial > repos > trinity_ctat > align_and_estimate_abundance

comparison trinityToolWrapper.py @ 0:a9723c18d389 draft

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Adding align_and_estimate_abundance tool.
author trinity_ctat
date Thu, 21 Sep 2017 15:11:18 -0400
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children 9e5c3f162eca
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-1:000000000000 0:a9723c18d389
1 #!/usr/bin/env python
2
3
4 # borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools.
5
6 """
7 Wrapper that execute a program and its arguments but reports standard error
8 messages only if the program exit status was not 0
9 Example: ./stderr_wrapper.py myprog arg1 -f arg2
10 """
11
12 import sys, subprocess, os
13
14 assert sys.version_info[:2] >= ( 2, 4 )
15
16 TRINITY_BASE_DIR = ""
17 if os.environ.has_key('TRINITY_HOME'):
18 TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
19 else:
20 # Cicada Dennis added looking for the location of the Trinity program using the unix "which" utility.
21 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
22 try:
23 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
24 except:
25 t, v, tb = sys.exc_info()
26 sys.stderr.write("You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running this");
27 raise t, v, tb
28 else:
29 output1, err1 = pipe1.communicate()
30 # Take off the last part of the path (which is the Trinity command)
31 TRINITY_BASE_DIR = "/".join(output1.split("/")[0:-1])
32
33 # get bindir
34 bindir = sys.argv[0]
35 bindir = bindir.split("/")
36 if len(bindir) > 1:
37 bindir.pop()
38 bindir = "/".join(bindir)
39 else:
40 bindir = "."
41
42
43 ## add locations of tools to path setting.
44 TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt";
45 for line in open(TOOL_PATHS_FILE):
46 line = line.rstrip()
47 os.environ['PATH'] += ":" + line
48
49
50 def stop_err( msg ):
51 sys.stderr.write( "%s\n" % msg )
52 sys.exit()
53
54 def __main__():
55 # Get command-line arguments
56 args = sys.argv
57 # Remove name of calling program, i.e. ./stderr_wrapper.py
58 args.pop(0)
59 # If there are no arguments left, we're done
60 if len(args) == 0:
61 return
62
63 # If one needs to silence stdout
64 #args.append( ">" )
65 #args.append( "/dev/null" )
66
67 args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]);
68
69 cmdline = " ".join(args)
70
71
72
73 try:
74 # Run program
75 err_capture = open("stderr.txt", 'w')
76 proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout )
77 returncode = proc.wait()
78 err_capture.close()
79
80
81 if returncode != 0:
82 raise Exception
83
84 except Exception:
85 # Running Grinder failed: write error message to stderr
86 err_text = open("stderr.txt").readlines()
87 stop_err( "ERROR:\n" + "\n".join(err_text))
88
89
90 if __name__ == "__main__": __main__()