diff trinityrnaseq_protocol/EdgeR_differentialExpression_wrapper.py @ 0:1c37a8003755 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityrnaseq_protocol/EdgeR_differentialExpression_wrapper.py	Mon Sep 28 22:44:29 2015 -0400
@@ -0,0 +1,40 @@
+import sys, os, subprocess
+
+TRINITY_BASE_DIR = ""
+if os.environ.has_key('TRINITY_HOME'):
+    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
+else:
+    sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
+    sys.exit(1)
+
+usage= "usage: " + " $counts_matrix" + " $dispersion"
+
+if len(sys.argv)<2:
+    print "Require atleast two parameters"
+else:
+    print "All good- command going ahead"
+print " "
+
+def run_command(cmd):
+    print "The command used: " + cmd
+    pipe=subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
+    pipe.wait()
+    ret= pipe.returncode
+    if ret:
+        print "command died: " + str(ret)
+        print pipe.stderr.readlines()
+        sys.exit(1)
+    else:
+        return
+print " "
+
+countmatrix= "counts_matrix"
+
+cmd= "cp " + sys.argv[1] + " " + countmatrix 
+run_command(cmd)
+
+cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir"
+
+run_command(cmd)
+
+sys.exit(0)