--- a/prince_postprocess.py	Mon Oct 29 08:30:06 2018 -0400
+++ b/prince_postprocess.py	Tue Nov 13 12:19:53 2018 -0500
@@ -8,8 +8,8 @@
 
 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('-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)
@@ -18,6 +18,19 @@
 
 #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:
@@ -25,8 +38,9 @@
 		index = 0
 		for line in prince_output:
 			if x%2 == 0:
-                                sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.sample[index])
-				output.write(re.sub('.*.dat', sample, line))
+				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)