--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctat_abundance_estimation_to_matrix.py	Tue Jul 17 11:47:32 2018 -0400
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+
+import sys, os, string, subprocess
+
+#aliasing the filenames using the labels
+
+
+def run_command(command):
+    print "Running command: " + command
+    
+    err_capture_file = open("my.stderr", 'w') # writing stderr to a file
+    cmd_run = subprocess.Popen(args=command, shell=True, stderr=err_capture_file, stdout=sys.stdout)
+    err = cmd_run.wait() # get exit code from command execution
+    err_capture_file.close()
+
+    if err:
+        # report the error messages we captured, and exit non-zero
+        sys.stderr.write("Error, cmd: " + command + " died with ret: " + `err`)
+        for line in open(err_capture_file):
+            sys.stderr.write(line)
+        sys.exit(err)
+    return
+
+label_list = []  # symlink files to the labels
+for i in range(1, len(sys.argv), 2):
+    filename=sys.argv[i]
+    label= sys.argv[i+1]
+    cmd= "ln -sf " + filename + " " + label
+    label_list.append(label)
+    run_command(cmd)
+
+
+# run the abundance estimation script
+
+cmd = os.path.dirname(sys.argv[0]) + "/ctat_trinity_tool_wrapper.py " + " util/abundance_estimates_to_matrix.pl --gene_trans_map none --est_method RSEM --cross_sample_norm TMM " + " ".join(label_list)
+
+run_command(cmd)
+
+sys.exit(0)
+