--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spotyping_postprocess.py	Tue Nov 13 10:46:18 2018 -0500
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+
+import sys
+import argparse as ap
+import re
+parser = ap.ArgumentParser(prog='spotyping_postprocess', conflict_handler='resolve',
+                           description="Postprocess galaxy spotyping output")
+
+input = parser.add_argument_group('Input', '')
+input.add_argument('-s', '--sample', nargs='+', required=True, help="Sample names")
+input.add_argument('-f', '--file', nargs='+', required=True, help="File of spotyping in galaxy convention")
+if len(sys.argv) == 0:
+    parser.print_usage()
+    sys.exit(1)
+
+args = parser.parse_args()
+
+
+sample_dict={}
+
+
+with open('spotyping_postprocess_output.txt', 'w') as output:
+	index = 0
+	for path in args.file:
+		with open(path) as f:
+			for line in f:
+				#sample_dict[re.sub(".*/","",line.rstrip())] = args.sample[path_index]
+				sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.sample[index].rstrip().lstrip())
+				output.write(re.sub(".*.dat", sample, line))
+		index += 1
+