Mercurial > repos > trinity_ctat > ctat_edger_differential_expression

comparison ctat_edger_differential_expression.py @ 0:f36264827fb4 draft default tip

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author trinity_ctat
date Tue, 17 Jul 2018 11:52:09 -0400
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-1:000000000000 0:f36264827fb4
1 import sys, os, subprocess
2
3 TRINITY_BASE_DIR = ""
4 if os.environ.has_key('TRINITY_HOME'):
5 TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
6 elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions of python.
7 # 2017-09-26
8 # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
9 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
10 # I also found distutils.spawn.find_executable() which might work, but already implemented the below.
11 try:
12 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
13 except:
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])
15 sys.stderr.write(msg)
16 # t, v, tb = sys.exc_info()
17 # raise t, v, tb
18 # For some reason the above was giving a syntax error.
19 # A simple raise should reraise the existing exception.
20 raise
21 else:
22 TrinityPath, err_info = pipe1.communicate()
23 # FIX - probably should be checking err_info for errors...
24 # Determine the TRINITY_BASE_DIR from output1.
25 # If TrinityPath is a link, we need to dereference the link.
26 TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
27 # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
28 # print os.path.islink(TrinityPath)
29 TrinityPath = os.path.abspath(TrinityPath)
30 # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
31 # print msg
32 # print os.path.islink(TrinityPath)
33 while os.path.islink(TrinityPath):
34 # print "That path is a link."
35 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
36 # print "The new path is: {:s}".format(TrinityPath)
37 # Take off the last part of the path (which is the Trinity command)
38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
39 else:
40 sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, " + \
41 "or ensure that directory is in the PATH before running.")
42 sys.exit(1)
43
44 usage= "usage: " + " $counts_matrix" + " $dispersion"
45
46 if len(sys.argv)<2:
47 print "Require at least two parameters, " + usage
48 else:
49 print "All good- command going ahead"
50 print " "
51
52 def run_command(cmd):
53 # 2017-10-02
54 # Cicada Dennis put the subprocess command in a try/except statement.
55 # Errors were going undetected the way it was written previously.
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
67 if ret:
68 print "command died: " + str(ret)
69 sys.stderr.write(cmd_stderr)
70 sys.exit(ret)
71 else:
72 # Any error output is written to stdout instead of stderr, since no error has occurred.
73 sys.stderr.write(cmd_stderr)
74 return
75
76 print ""
77
78 countmatrix= "counts_matrix"
79
80 cmd= "cp " + sys.argv[1] + " " + countmatrix
81 run_command(cmd)
82
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"
84
85 run_command(cmd)
86
87 sys.exit(0)