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1 import sys, os, subprocess
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2
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3 TRINITY_BASE_DIR = ""
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4 if os.environ.has_key('TRINITY_HOME'):
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5 TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
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6 elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions of python.
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7 # 2017-09-26
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8 # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
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9 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
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10 # I also found distutils.spawn.find_executable() which might work, but already implemented the below.
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11 try:
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12 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
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13 except:
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14 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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15 sys.stderr.write(msg)
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16 # t, v, tb = sys.exc_info()
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17 # raise t, v, tb
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18 # For some reason the above was giving a syntax error.
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19 # A simple raise should reraise the existing exception.
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20 raise
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21 else:
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22 TrinityPath, err_info = pipe1.communicate()
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23 # FIX - probably should be checking err_info for errors...
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24 # Determine the TRINITY_BASE_DIR from output1.
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25 # If TrinityPath is a link, we need to dereference the link.
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26 TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
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27 # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
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28 # print os.path.islink(TrinityPath)
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29 TrinityPath = os.path.abspath(TrinityPath)
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30 # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
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31 # print msg
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32 # print os.path.islink(TrinityPath)
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33 while os.path.islink(TrinityPath):
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34 # print "That path is a link."
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35 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
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36 # print "The new path is: {:s}".format(TrinityPath)
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37 # Take off the last part of the path (which is the Trinity command)
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38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
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39 else:
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40 sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, " + \
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41 "or ensure that directory is in the PATH before running.")
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42 sys.exit(1)
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43
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44 usage= "usage: " + " $counts_matrix" + " $dispersion"
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45
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46 if len(sys.argv)<2:
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47 print "Require at least two parameters, " + usage
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48 else:
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49 print "All good- command going ahead"
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50 print " "
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51
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52 def run_command(cmd):
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53 # 2017-10-02
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54 # Cicada Dennis put the subprocess command in a try/except statement.
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55 # Errors were going undetected the way it was written previously.
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56 print "Running command:\n\t" + cmd
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57 try:
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58 pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
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59 cmd_stdout, cmd_stderr = pipe.communicate()
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60 except:
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61 msg = "ERROR while running command:\n\t" + cmd
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62 sys.stderr.write(msg)
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63 raise
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64
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65 sys.stdout.write(cmd_stdout)
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66 ret = pipe.returncode
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67 if ret:
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68 print "command died: " + str(ret)
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69 sys.stderr.write(cmd_stderr)
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70 sys.exit(ret)
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71 else:
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72 # Any error output is written to stdout instead of stderr, since no error has occurred.
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73 sys.stderr.write(cmd_stderr)
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74 return
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75
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76 print ""
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77
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78 countmatrix= "counts_matrix"
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79
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80 cmd= "cp " + sys.argv[1] + " " + countmatrix
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81 run_command(cmd)
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82
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83 cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir"
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84
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85 run_command(cmd)
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86
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87 sys.exit(0)
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