--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctat_analyze_differential_expression.py	Tue Jul 17 11:49:33 2018 -0400
@@ -0,0 +1,123 @@
+import sys, os, subprocess
+
+TRINITY_BASE_DIR = ""
+if os.environ.has_key('TRINITY_HOME'):
+    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
+elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions of python.
+    # 2017-09-26
+    # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
+    # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
+    # I also found distutils.spawn.find_executable() which might work, but already implemented the below.
+    try:
+        pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
+    except:
+        msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.\n".format(sys.argv[0])
+        sys.stderr.write(msg)
+        # t, v, tb = sys.exc_info()
+        # raise t, v, tb
+        # For some reason the above was giving a syntax error. 
+        # A simple raise should reraise the existing exception.
+        raise
+    else:
+        TrinityPath, err_info = pipe1.communicate()
+        # FIX - probably should be checking err_info for errors...
+        # Determine the TRINITY_BASE_DIR from output1.
+        # If TrinityPath is a link, we need to dereference the link.
+        TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
+        # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
+        # print os.path.islink(TrinityPath)
+        TrinityPath = os.path.abspath(TrinityPath)
+        # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
+        # print msg
+        # print os.path.islink(TrinityPath)
+        while os.path.islink(TrinityPath):
+            # print "That path is a link."
+            TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
+            # print "The new path is: {:s}".format(TrinityPath)
+        # Take off the last part of the path (which is the Trinity command)
+        TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
+else:
+    sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.")
+    sys.exit(1)
+
+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):
+    # 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()
+    except:
+        msg = "ERROR while running command:\n\t" + cmd
+        sys.stderr.write(msg)
+        raise
+    
+    sys.stdout.write(cmd_stdout)
+    ret = pipe.returncode
+    if ret:
+        print "command died: " + str(ret)
+        sys.stderr.write(cmd_stderr)
+        sys.exit(ret)
+    else:
+        # 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 -xvf " + Final_tar_gz)
+
+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
+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.centered.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.centered.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)