Mercurial > repos > tyty > structurefold
comparison upload/Iterative_mapping/truncate.py @ 34:d74ed492efdd draft
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author | tyty |
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date | Mon, 20 Oct 2014 14:55:16 -0400 |
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33:1a92d934f8d1 | 34:d74ed492efdd |
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1 #!/usr/bin/env python | |
2 # -*- coding: utf-8 -*- | |
3 | |
4 import sys | |
5 from Bio import SeqIO | |
6 | |
7 fasta_file = sys.argv[1] | |
8 shift_in = sys.argv[2] | |
9 result_file = sys.argv[3] | |
10 length = sys.argv[4] | |
11 | |
12 shift = int(shift_in) | |
13 | |
14 fasta_sequences = SeqIO.parse(open(fasta_file),'fasta'); | |
15 h = file(result_file,'w') | |
16 for seq in fasta_sequences: | |
17 nuc = seq.id; | |
18 sequence = seq.seq.tostring(); | |
19 if (len(sequence)-shift)>=int(length): | |
20 h.write('>'+nuc) | |
21 h.write('\n') | |
22 h.write(sequence[0:(len(sequence)-shift)]) | |
23 h.write('\n') | |
24 | |
25 | |
26 | |
27 | |
28 h.close() | |
29 | |
30 | |
31 | |
32 |