Mercurial > repos > tyty > structurefold
comparison Iterative_mapping/seq_track.py @ 30:4d81d174dece draft
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author | tyty |
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date | Mon, 20 Oct 2014 14:44:01 -0400 |
parents | d56631911cc1 |
children |
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29:003096bd038c | 30:4d81d174dece |
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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 | |
36 | |
37 | |
38 |