--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/format_reago_input_files.py	Tue Dec 08 10:35:06 2015 -0500
@@ -0,0 +1,34 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+import sys
+import os
+import argparse
+import re
+
+reago_dir = '/tools/rna_manipulation/reago/reago/'
+
+def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
+    to_add = '.' + str(read_pair_num)
+    with open(input_filepath,'r') as input_file:
+        with open(output_filepath,'w') as output_file:
+            for line in input_file:
+                if line[0] == '>':
+                    split_line = line.split()
+                    seq_id = split_line[0]
+                    if seq_id.rfind(to_add) != (len(seq_id)-len(to_add)):
+                        split_line[0] = seq_id + to_add
+                    output_file.write(' '.join(split_line) + '\n')
+                else:
+                    output_file.write(line)
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--r1_input', required=True)
+    parser.add_argument('--r2_input', required=True)
+    parser.add_argument('--r1_output', required=True)
+    parser.add_argument('--r2_output', required=True)
+    args = parser.parse_args()
+
+    add_read_pair_num(args.r1_input, args.r1_output, 1)
+    add_read_pair_num(args.r2_input, args.r2_output, 2)
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