--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prince_postprocess.py	Tue Nov 13 11:41:37 2018 -0500
@@ -0,0 +1,50 @@
+#!/usr/bin/env python
+
+import sys
+import argparse as ap
+import re
+parser = ap.ArgumentParser(prog='prince_postprocess', conflict_handler='resolve',
+                           description="Postprocess galaxy PRINCE output")
+
+input = parser.add_argument_group('Input', '')
+input.add_argument('-i', '--input', nargs=1, required=True, help="PRINCE OUTPUT")
+input.add_argument('-s', '--sample', nargs='+', required=True, help="Sample names")
+input.add_argument('-f', '--file', nargs='+', required=True, help="File of forward reads in galaxy convention")
+if len(sys.argv) == 0:
+    parser.print_usage()
+    sys.exit(1)
+
+args = parser.parse_args()
+
+#print(args.input)
+#sample_name = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.label.rstrip().lstrip())
+sample_dict={}
+path_index = 0
+for path in args.file:
+	with open(path) as f:
+		for line in f:
+			sample_dict[re.sub(".*/","",line)] = sample[path_index]
+	path_index += 1
+			
+			
+
+
+
+
+
+with open(args.input[0]) as prince_output:
+	with open('prince_postprocess_output.txt', 'w') as output:
+		x = 1
+		index = 0
+		for line in prince_output:
+			if x%2 == 0:
+				entries =line.rstrip().split(',')
+                                sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', sample_dict[entries[0]])
+				output.write(re.sub(entries[0], sample, line))
+				index += 1
+			else:
+				output.write(line)
+			x += 1
+		#output.write("\n")
+
+