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11
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1 '''
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2 change start and end of interval files
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3 '''
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4
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5 import sys
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6
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7 def resize(infile,outfile,expr_start,expr_end,strand):
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8 fin = open(infile)
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9 fout = open(outfile,'w')
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10 if expr_start[0:3] == 'end':
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11 c1 = 2
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12 n1 = int(expr_start[3:])
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13 else:
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14 c1 = 1
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15 n1 = int(expr_start[5:])
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16 if expr_end[0:3] == 'end':
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17 c2 = 2
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18 n2 = int(expr_end[3:])
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19 else:
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20 c2 = 1
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21 n2 = int(expr_end[5:])
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22 if strand == 'ignore':
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23 for line in fin:
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24 flds = line.strip().split('\t')
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25 start = int(flds[c1]) + n1
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26 if start >= 0:
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27 end = int(flds[c2]) + n2
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28 if end >= start:
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29 flds[1] = str(start)
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30 flds[2] = str(end)
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31 fout.write('\t'.join(flds)+'\n')
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32 else:# upstream downstream
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33 for line in fin:
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34 flds = line.strip().split('\t')
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35 if flds[5] == '+':
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36 start = int(flds[c1]) + n1
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37 if start >= 0:
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38 end = int(flds[c2]) + n2
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39 if end >= start:
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40 flds[1] = str(start)
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41 flds[2] = str(end)
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42 fout.write('\t'.join(flds)+'\n')
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43 else: # on the - strand
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44 start = int(flds[3-c2]) - n2 # end=end+n2
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45 if start >= 0:
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46 end = int(flds[3-c1]) - n1
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47 if end >= start:
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48 flds[1] = str(start)
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49 flds[2] = str(end)
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50 fout.write('\t'.join(flds)+'\n')
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51 fin.close()
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52 fout.close()
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53
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54 if __name__ == "__main__":
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55 resize(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5])
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56 # python resize.py in.bed out.bed start-3 end+5 both
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57 # python resize.py <input.bed> <output.bed> expr_start expr_end strand(both/+/-)
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