Mercurial > repos > trinity_ctat > align_and_estimate_abundance
view trinityToolWrapper.py @ 3:32b6a47c9312 draft
Fix python syntax error.
author | trinity_ctat |
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date | Tue, 26 Sep 2017 11:43:35 -0400 |
parents | 9e5c3f162eca |
children | cb71c6b0bf66 |
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#!/usr/bin/env python # borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools. """ Wrapper that execute a program and its arguments but reports standard error messages only if the program exit status was not 0 Example: ./stderr_wrapper.py myprog arg1 -f arg2 """ import sys, subprocess, os assert sys.version_info[:2] >= ( 2, 4 ) TRINITY_BASE_DIR = "" if os.environ.has_key('TRINITY_HOME'): TRINITY_BASE_DIR = os.environ['TRINITY_HOME']; else: # 2017-09-26 # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility. # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that. # I just found distutils.spawn.find_executable() which might work, but already implemented the below. try: pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE) except: t, v, tb = sys.exc_info() 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])) raise t, v, tb else: TrinityPath, err_info = pipe1.communicate() # FIX - probably should be checking err_info for errors... # Determine the TRINITY_BASE_DIR from output1. # If TrinityPath is a link, we need to dereference the link. while os.path.islink(TrinityPath) TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath)) # Take off the last part of the path (which is the Trinity command) TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) # get bindir bindir = sys.argv[0] bindir = bindir.split("/") if len(bindir) > 1: bindir.pop() bindir = "/".join(bindir) else: bindir = "." ## add locations of tools to path setting. TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt"; for line in open(TOOL_PATHS_FILE): line = line.rstrip() os.environ['PATH'] += ":" + line 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" ) args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]); cmdline = " ".join(args) try: # Run program err_capture = open("stderr.txt", 'w') proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout ) returncode = proc.wait() err_capture.close() if returncode != 0: raise Exception except Exception: # Running Grinder failed: write error message to stderr err_text = open("stderr.txt").readlines() stop_err( "ERROR:\n" + "\n".join(err_text)) if __name__ == "__main__": __main__()