Mercurial > repos > bebatut > reago

comparison format_reago_input_files.py @ 0:04749f9173e5 draft default tip

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
author bebatut
date Tue, 08 Dec 2015 10:35:06 -0500
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-1:000000000000 0:04749f9173e5
1 #!/usr/bin/python
2 # -*- coding: utf-8 -*-
3
4 import sys
5 import os
6 import argparse
7 import re
8
9 reago_dir = '/tools/rna_manipulation/reago/reago/'
10
11 def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
12 to_add = '.' + str(read_pair_num)
13 with open(input_filepath,'r') as input_file:
14 with open(output_filepath,'w') as output_file:
15 for line in input_file:
16 if line[0] == '>':
17 split_line = line.split()
18 seq_id = split_line[0]
19 if seq_id.rfind(to_add) != (len(seq_id)-len(to_add)):
20 split_line[0] = seq_id + to_add
21 output_file.write(' '.join(split_line) + '\n')
22 else:
23 output_file.write(line)
24
25 if __name__ == '__main__':
26 parser = argparse.ArgumentParser()
27 parser.add_argument('--r1_input', required=True)
28 parser.add_argument('--r2_input', required=True)
29 parser.add_argument('--r1_output', required=True)
30 parser.add_argument('--r2_output', required=True)
31 args = parser.parse_args()
32
33 add_read_pair_num(args.r1_input, args.r1_output, 1)
34 add_read_pair_num(args.r2_input, args.r2_output, 2)