# HG changeset patch
# User trinity_ctat
# Date 1506969543 14400
# Node ID dab3b085f23d06bc8100709b862c054c2a70cc23
# Parent  08f897c2b57eaa5b490c4b70f749df1ec6e6cc2c
Adding more debugging statements.

diff -r 08f897c2b57e -r dab3b085f23d analyze_diff_exp_wrapper.py
--- a/analyze_diff_exp_wrapper.py	Mon Oct 02 13:53:09 2017 -0400
+++ b/analyze_diff_exp_wrapper.py	Mon Oct 02 14:39:03 2017 -0400
@@ -59,6 +59,7 @@
     # 2017-10-02
     # Cicada Dennis put the subprocess command in a try/except statement.
     # Errors were going undetected the way it was written previously.
+    print "Running command:\n\t" + cmd
     try:
         pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
         cmd_stdout, cmd_stderr = pipe.communicate()
@@ -74,21 +75,30 @@
         sys.stderr.write(cmd_stderr)
         sys.exit(ret)
     else:
-        # Any error output written to stdout instead of stderr, since no error has occurred.
+        # Any error output is written to stdout instead of stderr, since no error has occurred.
         sys.stderr.write(cmd_stderr) 
         return
 
 print ""
 Final_tar_gz= "edgeR.tar.gz"
 run_command("cp "+ sys.argv[1] + " " + Final_tar_gz)
-run_command("tar -xzvf " + Final_tar_gz)
-run_command("mv " + "edgeR_results" + "/* ." )
+run_command("tar -xvf " + Final_tar_gz)
 
-print ""
+print "Before moving files."
 run_command("pwd")
 run_command("ls -lad ./*")
 print "\nedgeR_results/"
 run_command("ls -la edgeR_results")
+print ""
+
+run_command("mv edgeR_results /* ." )
+
+print "After moving files."
+run_command("pwd")
+run_command("ls -lad ./*")
+print "\nedgeR_results/"
+run_command("ls -la edgeR_results")
+print ""
 
 # run the analyze command
 cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " +  Normalized_Matrix + " -P " +  Pvalue + " -C " + Cvalue