Mercurial > repos > trinity_ctat > align_and_estimate_abundance
annotate trinityToolWrapper.py @ 3:32b6a47c9312 draft
Fix python syntax error.
| author | trinity_ctat |
|---|---|
| date | Tue, 26 Sep 2017 11:43:35 -0400 |
| parents | 9e5c3f162eca |
| children | cb71c6b0bf66 |
| rev | line source |
|---|---|
| 0 | 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: | |
|
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9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
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20 # 2017-09-26 |
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9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
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21 # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility. |
| 0 | 22 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that. |
|
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9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
parents:
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23 # I just found distutils.spawn.find_executable() which might work, but already implemented the below. |
| 0 | 24 try: |
| 25 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE) | |
| 26 except: | |
| 27 t, v, tb = sys.exc_info() | |
| 3 | 28 sys.stderr.write("You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.".format(sys.argv[0])) |
| 0 | 29 raise t, v, tb |
| 30 else: | |
|
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9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
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31 TrinityPath, err_info = pipe1.communicate() |
|
9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
parents:
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changeset
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32 # FIX - probably should be checking err_info for errors... |
|
9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
parents:
0
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changeset
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33 # Determine the TRINITY_BASE_DIR from output1. |
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9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
parents:
0
diff
changeset
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34 # If TrinityPath is a link, we need to dereference the link. |
|
9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
parents:
0
diff
changeset
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35 while os.path.islink(TrinityPath) |
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9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
parents:
0
diff
changeset
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36 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath)) |
| 0 | 37 # Take off the last part of the path (which is the Trinity command) |
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2
9e5c3f162eca
Needed to dereference links when searching for TRINITY_BASE_DIR.
trinity_ctat
parents:
0
diff
changeset
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38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) |
| 0 | 39 |
| 40 # get bindir | |
| 41 bindir = sys.argv[0] | |
| 42 bindir = bindir.split("/") | |
| 43 if len(bindir) > 1: | |
| 44 bindir.pop() | |
| 45 bindir = "/".join(bindir) | |
| 46 else: | |
| 47 bindir = "." | |
| 48 | |
| 49 | |
| 50 ## add locations of tools to path setting. | |
| 51 TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt"; | |
| 52 for line in open(TOOL_PATHS_FILE): | |
| 53 line = line.rstrip() | |
| 54 os.environ['PATH'] += ":" + line | |
| 55 | |
| 56 | |
| 57 def stop_err( msg ): | |
| 58 sys.stderr.write( "%s\n" % msg ) | |
| 59 sys.exit() | |
| 60 | |
| 61 def __main__(): | |
| 62 # Get command-line arguments | |
| 63 args = sys.argv | |
| 64 # Remove name of calling program, i.e. ./stderr_wrapper.py | |
| 65 args.pop(0) | |
| 66 # If there are no arguments left, we're done | |
| 67 if len(args) == 0: | |
| 68 return | |
| 69 | |
| 70 # If one needs to silence stdout | |
| 71 #args.append( ">" ) | |
| 72 #args.append( "/dev/null" ) | |
| 73 | |
| 74 args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]); | |
| 75 | |
| 76 cmdline = " ".join(args) | |
| 77 | |
| 78 | |
| 79 | |
| 80 try: | |
| 81 # Run program | |
| 82 err_capture = open("stderr.txt", 'w') | |
| 83 proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout ) | |
| 84 returncode = proc.wait() | |
| 85 err_capture.close() | |
| 86 | |
| 87 | |
| 88 if returncode != 0: | |
| 89 raise Exception | |
| 90 | |
| 91 except Exception: | |
| 92 # Running Grinder failed: write error message to stderr | |
| 93 err_text = open("stderr.txt").readlines() | |
| 94 stop_err( "ERROR:\n" + "\n".join(err_text)) | |
| 95 | |
| 96 | |
| 97 if __name__ == "__main__": __main__() |