annotate Iterative_mapping/seq_track.py @ 62:58df1060fea1 draft

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author tyty
date Tue, 18 Nov 2014 15:53:42 -0500
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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4 import sys
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5 from read_file import *
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6 from Bio import SeqIO
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8 unmap_file = sys.argv[1]
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9 reads_file = sys.argv[2]
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10 result_file = sys.argv[3]
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11 tp = sys.argv[4]
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14 unmap = read_t_file(unmap_file);
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16 h = file(result_file, 'w')
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18 reads = SeqIO.parse(reads_file,tp)
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19 um = set()
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20 for i in range(0, len(unmap)):
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21 id_r = unmap[i][0]
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22 um.add(id_r)
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24 for read in reads:
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25 if read.id in um:
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26 h.write('>')
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27 h.write(read.id)
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28 h.write('\n')
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29 h.write(read.seq.tostring())
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30 h.write('\n')
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34 h.close()
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