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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, or ensure that directory is in the PATH before running.")
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41 sys.exit(1)
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42
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43 usage= "usage: " + sys.argv[0] + " " + "edgeR.tar.gz " + "TMM_normalized_FPKM_matrix " + "P-value " + "C-value"
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44 print sys.argv
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45 print usage
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46 print " "
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47
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48 if len(sys.argv)<5:
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49 print "Require atleast two parameters"
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50 else:
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51 print "All good- command going ahead"
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52 print " "
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53
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54 Normalized_Matrix=sys.argv[2]
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55 Pvalue=sys.argv[3]
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56 Cvalue=sys.argv[4]
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57
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58 def run_command(cmd):
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59 # 2017-10-02
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60 # Cicada Dennis put the subprocess command in a try/except statement.
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61 # Errors were going undetected the way it was written previously.
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62 print "Running command:\n\t" + cmd
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63 try:
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64 pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
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65 cmd_stdout, cmd_stderr = pipe.communicate()
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66 except:
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67 msg = "ERROR while running command:\n\t" + cmd
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68 sys.stderr.write(msg)
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69 raise
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70
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71 sys.stdout.write(cmd_stdout)
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72 ret = pipe.returncode
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73 if ret:
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74 print "command died: " + str(ret)
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75 sys.stderr.write(cmd_stderr)
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76 sys.exit(ret)
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77 else:
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78 # Any error output is written to stdout instead of stderr, since no error has occurred.
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79 sys.stderr.write(cmd_stderr)
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80 return
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81
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82 print ""
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83 Final_tar_gz= "edgeR.tar.gz"
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84 run_command("cp "+ sys.argv[1] + " " + Final_tar_gz)
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85 run_command("tar -xvf " + Final_tar_gz)
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86
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87 print "Before moving files."
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88 run_command("pwd")
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89 run_command("ls -lad ./*")
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90 print "\nedgeR_results/"
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91 run_command("ls -la edgeR_results")
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92 print ""
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93
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94 run_command("mv edgeR_results/* ." )
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95
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96 print "After moving files."
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97 run_command("pwd")
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98 run_command("ls -lad ./*")
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99 print "\nedgeR_results/"
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100 run_command("ls -la edgeR_results")
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101 print ""
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102
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103 # run the analyze command
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104 cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue
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105 run_command(cmd)
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106
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107 origMatrixName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix"
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108 # diffExpr.P0.001_C2.0.matrix
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109 run_command("mv " + origMatrixName + " diffExpr.matrix")
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110
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111 SampleCorName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.sample_cor.dat"
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112 # diffExpr.P0.001_C2.0.matrix.log2.sample_cor.dat
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113 run_command("mv " + SampleCorName + " diffExpr.matrix.log2..sample_cor.dat")
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114
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115 CorMatrix= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.sample_cor_matrix.pdf"
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116 # diffExpr.P0.001_C2.0.matrix.log2.sample_cor_matrix.pdf
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117 run_command("mv " + CorMatrix + " diffExpr.matrix.log2.sample_cor_matrix.pdf")
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118
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119 Heatmap= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.genes_vs_samples_heatmap.pdf"
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120 #diffExpr.P0.001_C2.0.matrix.log2.centered.genes_vs_samples_heatmap.pdf
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121 run_command("mv " + Heatmap + " diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf")
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122
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123 sys.exit(0)
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