Mercurial > repos > trinity_ctat > ctat_abundance_estimation_to_matrix

annotate ctat_trinity_tool_wrapper.py @ 3:ecf4d2a21553 draft

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testing
author trinity_ctat
date Mon, 18 Jun 2018 16:10:06 -0400
parents b59a36e94b0e
children
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0
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1 #!/usr/bin/env python
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2
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3
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4 # borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools.
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5
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6 """
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7 Wrapper that execute a program and its arguments but reports standard error
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8 messages only if the program exit status was not 0
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9 Example: ./stderr_wrapper.py myprog arg1 -f arg2
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10 """
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11
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12 import sys, subprocess, os
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13 print sys.version
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14
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15 assert sys.version_info[:2] >= ( 2, 4 )
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16
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17 TRINITY_BASE_DIR = ""
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18 if os.environ.has_key('TRINITY_HOME'):
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19 TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
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20 elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions.
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21 # 2017-09-26
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22 # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
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23 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
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24 # I just found distutils.spawn.find_executable() which might work, but already implemented the below.
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25 try:
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26 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
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27 except:
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28 msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.\n".format(sys.argv[0])
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29 sys.stderr.write(msg)
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30 # t, v, tb = sys.exc_info()
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31 # raise t, v, tb
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32 # For some reason the above was giving a syntax error.
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33 # A simple raise should reraise the existing exception.
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34 raise
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35 else:
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36 TrinityPath, err_info = pipe1.communicate()
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37 # FIX - probably should be checking err_info for errors...
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38 # Determine the TRINITY_BASE_DIR from output1.
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39 # If TrinityPath is a link, we need to dereference the link.
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40 TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
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41 # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
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42 # print os.path.islink(TrinityPath)
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43 TrinityPath = os.path.abspath(TrinityPath)
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44 # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
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45 # print msg
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46 # print os.path.islink(TrinityPath)
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47 while os.path.islink(TrinityPath):
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48 # print "That path is a link."
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49 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
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50 # print "The new path is: {:s}".format(TrinityPath)
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51 # Take off the last part of the path (which is the Trinity command)
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52 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
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53 else:
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54 sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.")
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55 sys.exit(1)
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56
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57
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58 # get bindir
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59 bindir = sys.argv[0]
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60 bindir = bindir.split("/")
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61 if len(bindir) > 1:
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62 bindir.pop()
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63 bindir = "/".join(bindir)
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64 else:
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65 bindir = "."
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66
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67
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68 ## add locations of tools to path setting.
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69 #TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt";
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70 #for line in open(TOOL_PATHS_FILE):
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71 # line = line.rstrip()
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72 # os.environ['PATH'] += ":" + line
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73
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74 # Add TrinityPath and its utils to the PATH environment variable.
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75 # print "Initially the PATH env variable is:\n\t{:s}".format(os.environ['PATH'])
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76 os.environ['PATH'] = os.environ['PATH'] + ":{:s}:{:s}".format(TRINITY_BASE_DIR,TRINITY_BASE_DIR+"/util")
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77 # print "Now the PATH env variable is:\n\t{:s}".format(os.environ['PATH'])
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78
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79
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80 def stop_err( msg ):
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81 sys.stderr.write( "%s\n" % msg )
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82 sys.exit()
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83
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84 def __main__():
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85 # Get command-line arguments
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86 args = sys.argv
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87 # Remove name of calling program, i.e. ./stderr_wrapper.py
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88 args.pop(0)
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89 # If there are no arguments left, we're done
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90 if len(args) == 0:
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91 return
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92
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93 # If one needs to silence stdout
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94 #args.append( ">" )
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95 #args.append( "/dev/null" )
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96 print "The TRINITY_BASE_DIR is:\n\t{:s}".format(TRINITY_BASE_DIR)
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97 print "The PATH env variable is:\n\t{:s}".format(os.environ['PATH'])
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98
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99 args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]);
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100
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101 cmdline = " ".join(args)
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102
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103 print "The command being invoked is:\n\t{:s}".format(cmdline)
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104
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105
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106 try:
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107 # Run program
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108 err_capture = open("stderr.txt", 'w')
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109 proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout )
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110 returncode = proc.wait()
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111 err_capture.close()
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112
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113
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114 if returncode != 0:
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115 raise Exception
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116
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117 except Exception:
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118 # Running Grinder failed: write error message to stderr
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119 err_text = open("stderr.txt").readlines()
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120 stop_err( "ERROR:\n" + "\n".join(err_text))
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121
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122
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parents:
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123 if __name__ == "__main__": __main__()