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comparison Iterative_mapping/truncate.py @ 71:b6bdd41440f3 draft

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author tyty
date Tue, 09 Dec 2014 03:02:27 -0500
parents 9d26c2e4953e
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70:f76deb490f06 71:b6bdd41440f3
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 t_end = sys.argv[5]
12
13 shift = int(shift_in)
14
15 fasta_sequences = SeqIO.parse(open(fasta_file),'fasta');
16 h = file(result_file,'w')
17 for seq in fasta_sequences:
18 nuc = seq.id;
19 sequence = seq.seq.tostring();
20 if (len(sequence)-shift)>=int(length):
21 h.write('>'+nuc)
22 h.write('\n')
23 if t_end == 'three_end':
24 h.write(sequence[0:(len(sequence)-shift)])
25 if t_end == 'five_end':
26 h.write(sequence[(shift):(len(sequence))])
27 h.write('\n')
28
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31
32 h.close()
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