ctat_analyze_differential_expression: ctat_analyze_diff_exp

annotate ctat_analyze_diff_exp_wrapper.py @ 0:6a8dadcd45e3 draft

Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.

author	trinity_ctat
date	Thu, 12 Apr 2018 10:10:11 -0400
parents
children

rev	line source
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	1 import sys, os, subprocess
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	2
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	3 TRINITY_BASE_DIR = ""
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	4 if os.environ.has_key('TRINITY_HOME'):
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	5 TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	6 elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions of python.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	7 # 2017-09-26
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	8 # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	9 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	10 # I also found distutils.spawn.find_executable() which might work, but already implemented the below.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	11 try:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	12 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	13 except:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	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])
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	15 sys.stderr.write(msg)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	16 # t, v, tb = sys.exc_info()
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	17 # raise t, v, tb
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	18 # For some reason the above was giving a syntax error.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	19 # A simple raise should reraise the existing exception.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	20 raise
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	21 else:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	22 TrinityPath, err_info = pipe1.communicate()
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	23 # FIX - probably should be checking err_info for errors...
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	24 # Determine the TRINITY_BASE_DIR from output1.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	25 # If TrinityPath is a link, we need to dereference the link.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	26 TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	27 # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	28 # print os.path.islink(TrinityPath)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	29 TrinityPath = os.path.abspath(TrinityPath)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	30 # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	31 # print msg
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	32 # print os.path.islink(TrinityPath)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	33 while os.path.islink(TrinityPath):
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	34 # print "That path is a link."
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	35 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	36 # print "The new path is: {:s}".format(TrinityPath)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	37 # Take off the last part of the path (which is the Trinity command)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	39 else:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	40 sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	41 sys.exit(1)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	42
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	43 usage= "usage: " + sys.argv[0] + " " + "edgeR.tar.gz " + "TMM_normalized_FPKM_matrix " + "P-value " + "C-value"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	44 print sys.argv
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	45 print usage
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	46 print " "
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	47
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	48 if len(sys.argv)<5:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	49 print "Require atleast two parameters"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	50 else:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	51 print "All good- command going ahead"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	52 print " "
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	53
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	54 Normalized_Matrix=sys.argv[2]
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	55 Pvalue=sys.argv[3]
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	56 Cvalue=sys.argv[4]
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	57
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	58 def run_command(cmd):
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	59 # 2017-10-02
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	60 # Cicada Dennis put the subprocess command in a try/except statement.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	61 # Errors were going undetected the way it was written previously.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	62 print "Running command:\n\t" + cmd
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	63 try:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	64 pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	65 cmd_stdout, cmd_stderr = pipe.communicate()
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	66 except:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	67 msg = "ERROR while running command:\n\t" + cmd
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	68 sys.stderr.write(msg)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	69 raise
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	70
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	71 sys.stdout.write(cmd_stdout)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	72 ret = pipe.returncode
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	73 if ret:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	74 print "command died: " + str(ret)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	75 sys.stderr.write(cmd_stderr)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	76 sys.exit(ret)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	77 else:
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	78 # Any error output is written to stdout instead of stderr, since no error has occurred.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	79 sys.stderr.write(cmd_stderr)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	80 return
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	81
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	82 print ""
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	83 Final_tar_gz= "edgeR.tar.gz"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	84 run_command("cp "+ sys.argv[1] + " " + Final_tar_gz)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	85 run_command("tar -xvf " + Final_tar_gz)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	86
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	87 print "Before moving files."
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	88 run_command("pwd")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	89 run_command("ls -lad ./*")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	90 print "\nedgeR_results/"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	91 run_command("ls -la edgeR_results")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	92 print ""
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	93
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	94 run_command("mv edgeR_results/* ." )
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	95
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	96 print "After moving files."
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	97 run_command("pwd")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	98 run_command("ls -lad ./*")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	99 print "\nedgeR_results/"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	100 run_command("ls -la edgeR_results")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	101 print ""
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	102
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	103 # run the analyze command
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	104 cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	105 run_command(cmd)
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	106
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	107 origMatrixName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	108 # diffExpr.P0.001_C2.0.matrix
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	109 run_command("mv " + origMatrixName + " diffExpr.matrix")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	110
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	111 SampleCorName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor.dat"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	112 # diffExpr.P0.001_C2.0.matrix.log2.sample_cor.dat
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	113 run_command("mv " + SampleCorName + " diffExpr.matrix.log2.sample_cor.dat")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	114
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	115 CorMatrix= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor_matrix.pdf"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	116 # diffExpr.P0.001_C2.0.matrix.log2.sample_cor_matrix.pdf
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	117 run_command("mv " + CorMatrix + " diffExpr.matrix.log2.sample_cor_matrix.pdf")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	118
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	119 Heatmap= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.genes_vs_samples_heatmap.pdf"
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	120 #diffExpr.P0.001_C2.0.matrix.log2.centered.genes_vs_samples_heatmap.pdf
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	121 run_command("mv " + Heatmap + " diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf")
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	122
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	123 sys.exit(0)

Mercurial > repos > trinity_ctat > ctat_analyze_differential_expression

annotate ctat_analyze_diff_exp_wrapper.py @ 0:6a8dadcd45e3 draft