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7
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1 '''
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2 #pattern name sequence name start stop score p-value q-value matched sequence
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3 constitutive-donor mm9_chr1_39533592_39535592_- 1815 1823 12.032 4.26e-06 0.397 CAGGTAAGT
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4 constitutive-donor mm9_chr1_59313750_59315750_+ 1889 1897 12.032 4.26e-06 0.397 CAGGTAAGT
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5
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6 #pattern name sequence name start stop score p-value q-value matched sequence
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7 constitutive-donor mm9_chr1_172019075_172021075_- 1947 1955 12.032 4.26e-06 0.843 CAGGTAAGT
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8 constitutive-donor mm9_chr1_15300532_15302532_+ 156 164 12.032 4.26e-06 0.843 CAGGTAAGT
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9 '''
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10
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11 import sys
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12
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13 def fimo2bed(filename,rc):
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14 '''
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15 parse fimo output to make a bed file
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16 rc: the sequence have been reverse complemented
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17 '''
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18 f = open(filename)
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19 header = f.readline()
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20 for line in f:
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21 pattern,posi,begin,stop,score,pv,qv,seq = line.strip().split('\t')
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22 flds = posi.split('_')
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23 start = flds[-3]
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24 end = flds[-2]
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25 strand = flds[-1]
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26 chrom = '_'.join(flds[1:-3]) #'chrX_random'
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27 if not rc:
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28 if strand == '+':
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29 start1 = str(int(start) + int(begin)-1)
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30 end1 = str(int(start) + int(stop))
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31 print '\t'.join([chrom,start1,end1,seq,score,strand])
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32 else:
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33 start1 = str(int(end) - int(stop))
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34 end1 = str(int(end) - int(begin)+1)
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35 print '\t'.join([chrom,start1,end1,seq,score,strand])
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36 else:
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37 if strand == '-':
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38 start1 = str(int(start) + int(begin)-1)
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39 end1 = str(int(start) + int(stop))
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40 print '\t'.join([chrom,start1,end1,seq,score,'+'])
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41 else:
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42 start1 = str(int(end) - int(stop))
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43 end1 = str(int(end) - int(begin)+1)
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44 print '\t'.join([chrom,start1,end1,seq,score,'-'])
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45
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46 fimo2bed(sys.argv[1],sys.argv[2]=='rc')
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