Mercurial > repos > trinity_ctat > edger_differential_expression

comparison EdgeR_differentialExpression_wrapper.py @ 3:70b3058d39d9 draft

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Adding more debugging statements.
author trinity_ctat
date Mon, 02 Oct 2017 14:36:31 -0400
parents 023628c034b6
children
comparison
equal deleted inserted replaced
2:93f07220f08c 3:70b3058d39d9
35 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath)) 35 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
36 # print "The new path is: {:s}".format(TrinityPath) 36 # print "The new path is: {:s}".format(TrinityPath)
37 # Take off the last part of the path (which is the Trinity command) 37 # Take off the last part of the path (which is the Trinity command)
38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) 38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
39 else: 39 else:
40 sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.") 40 sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, " + \
41 "or ensure that directory is in the PATH before running.")
41 sys.exit(1) 42 sys.exit(1)
42 43
43 usage= "usage: " + " $counts_matrix" + " $dispersion" 44 usage= "usage: " + " $counts_matrix" + " $dispersion"
44 45
45 if len(sys.argv)<2: 46 if len(sys.argv)<2:
47 else: 48 else:
48 print "All good- command going ahead" 49 print "All good- command going ahead"
49 print " " 50 print " "
50 51
51 def run_command(cmd): 52 def run_command(cmd):
52 print "The command used: " + cmd 53 # 2017-10-02
53 pipe=subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE) 54 # Cicada Dennis put the subprocess command in a try/except statement.
54 pipe.wait() 55 # Errors were going undetected the way it was written previously.
55 ret= pipe.returncode 56 print "Running command:\n\t" + cmd
57 try:
58 pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
59 cmd_stdout, cmd_stderr = pipe.communicate()
60 except:
61 msg = "ERROR while running command:\n\t" + cmd
62 sys.stderr.write(msg)
63 raise
64
65 sys.stdout.write(cmd_stdout)
66 ret = pipe.returncode
56 if ret: 67 if ret:
57 print "command died: " + str(ret) 68 print "command died: " + str(ret)
58 print pipe.stderr.readlines() 69 sys.stderr.write(cmd_stderr)
59 sys.exit(1) 70 sys.exit(ret)
60 else: 71 else:
72 # Any error output is written to stdout instead of stderr, since no error has occurred.
73 sys.stderr.write(cmd_stderr)
61 return 74 return
62 print " " 75
76 print ""
63 77
64 countmatrix= "counts_matrix" 78 countmatrix= "counts_matrix"
65 79
66 cmd= "cp " + sys.argv[1] + " " + countmatrix 80 cmd= "cp " + sys.argv[1] + " " + countmatrix
67 run_command(cmd) 81 run_command(cmd)
68 82
69 cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir" 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"
70
71 run_command(cmd) 84 run_command(cmd)
72 85
73 sys.exit(0) 86 sys.exit(0)