changeset 6:5fadb4b79378 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/analyze_diff_exp_wrapper.py	Wed Sep 23 15:21:54 2015 -0400
@@ -0,0 +1,63 @@
+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()
+
+usage= "usage: " + sys.argv[0] + " " + "edgeR.tar.gz " + "TMM_normalized_FPKM_matrix " + "P-value " + "C-value"
+print sys.argv 
+print usage 
+print " "
+
+if len(sys.argv)<5:
+	print "Require atleast two parameters"
+else:
+	print "All good- command going ahead"
+print " "
+
+Normalized_Matrix=sys.argv[2]
+Pvalue=sys.argv[3]
+Cvalue=sys.argv[4]
+
+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 " "
+
+Final_tar_gz= "edgeR.tar.gz"
+run_command("cp "+ sys.argv[1] + " " + "Final_tar_gz")
+run_command("tar -xvf " + "Final_tar_gz")
+run_command("mv " + "edgeR_results" + "/* ." )
+
+# run the analyze command
+cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " +  Normalized_Matrix + " -P " +  Pvalue + " -C " + Cvalue
+run_command(cmd)
+
+origMatrixName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix"
+# diffExpr.P0.001_C2.0.matrix
+run_command("mv " + origMatrixName + " diffExpr.matrix")
+
+SampleCorName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor.dat"
+# diffExpr.P0.001_C2.0.matrix.log2.sample_cor.dat
+run_command("mv " + SampleCorName + " diffExpr.matrix.log2.sample_cor.dat")
+
+CorMatrix= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor_matrix.pdf"
+# diffExpr.P0.001_C2.0.matrix.log2.sample_cor_matrix.pdf
+run_command("mv " + CorMatrix + " diffExpr.matrix.log2.sample_cor_matrix.pdf")
+
+Heatmap= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.genes_vs_samples_heatmap.pdf"
+#diffExpr.P0.001_C2.0.matrix.log2.centered.genes_vs_samples_heatmap.pdf
+run_command("mv " + Heatmap + " diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf")
+
+sys.exit(0)