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comparison Iterative_mapping/seq_track.py @ 0:d56631911cc1 draft

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author tyty
date Mon, 15 Sep 2014 14:41:13 -0400
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-1:000000000000 0:d56631911cc1
1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3
4 import sys
5 from read_file import *
6 from Bio import SeqIO
7
8 unmap_file = sys.argv[1]
9 reads_file = sys.argv[2]
10 result_file = sys.argv[3]
11 tp = sys.argv[4]
12
13
14 unmap = read_t_file(unmap_file);
15
16 h = file(result_file, 'w')
17
18 reads = SeqIO.parse(reads_file,tp)
19 um = set()
20 for i in range(0, len(unmap)):
21 id_r = unmap[i][0]
22 um.add(id_r)
23
24 for read in reads:
25 if read.id in um:
26 h.write('>')
27 h.write(read.id)
28 h.write('\n')
29 h.write(read.seq.tostring())
30 h.write('\n')
31
32
33
34 h.close()
35
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38