Mercurial > repos > test-svm > kmersvm_test

annotate kmersvm/scripts/split_genome.py @ 2:e8dcc2ed0f9f draft

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Included bugfix, README
author test-svm
date Sun, 05 Aug 2012 16:32:03 -0400
parents 66088269713e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 import os
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2 import os.path
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3 import sys
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4 import optparse
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5 import math
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6 import re
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7 from libkmersvm import *
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8
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9 def split(bed_file,options):
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10 split_f = open(options.output, 'w')
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11 incr = options.incr
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12 size = options.size
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13 file = open(bed_file, 'rb')
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14
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15 for line in file:
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16 (name,start,length) = line.split('\t')
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17 start = int(start)
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18 length = int(length)
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19 end = size + start
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20
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21 while True:
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22 coords = "".join([name,"\t",str(start),"\t",str(end),"\n"])
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23 split_f.write(coords)
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24 if end + incr >= length:
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25 end += incr-((end+incr)-length)
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26 start += incr
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27 coords = "".join([name,"\t",str(start),"\t",str(end),"\n"])
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28 split_f.write(coords)
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29 break
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30 else:
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31 start += incr
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32 end += incr
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33
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34
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35 def main(argv=sys.argv):
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36 usage = "usage: %prog <bed_file>"
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37 parser = optparse.OptionParser(usage=usage)
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38
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39 parser.add_option("-s", dest="size", type="int", \
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40 default=1000, help="set chunk size")
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41 parser.add_option("-i", dest="incr", type="int", \
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42 default=500, help="set overlap size")
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43 parser.add_option("-o", dest="output", default="split_genome_output.bed", \
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44 help="output BED file (default is split_genome_output.bed)")
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45
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46 (options, args) = parser.parse_args()
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47
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48 bed_file = args[0]
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49
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50 split(bed_file, options)
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51
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52 if __name__ == "__main__": main()