# HG changeset patch
# User trinity_ctat
# Date 1506963327 14400
# Node ID 6f54e220d0353e5555f99dec5a647a3e5a370974
# Parent  54f1735788688c000c92be73aa336a8888ef859d
Adding some debugging statements.

diff -r 54f173578868 -r 6f54e220d035 analyze_diff_exp_wrapper.py
--- a/analyze_diff_exp_wrapper.py	Mon Oct 02 11:53:20 2017 -0400
+++ b/analyze_diff_exp_wrapper.py	Mon Oct 02 12:55:27 2017 -0400
@@ -56,23 +56,29 @@
 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 " "
+    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(ret)
+    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" + "/* ." )
 
+print ""
+run_command("pwd")
+run_command("ls -lad ./*")
+print "\nedgeR_results"
+run_command("ls -lad 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)