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11
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1 '''
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2 collapse intervals
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3 '''
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4
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5 def collapseInterval_strand(filename):
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6 uniqintv = {}
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7 data = {}
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8 f = open(filename)
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9 header = f.readline()
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10 if 'chr' in header:
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11 flds = header.strip().split('\t')
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12 key = '\t'.join([flds[0],flds[1],flds[2],flds[5]])
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13 uniqintv[key] = 1
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14 data[key] = flds
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15 for line in f:
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16 flds = line.strip().split('\t')
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17 key = '\t'.join([flds[0],flds[1],flds[2],flds[5]])
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18 if uniqintv.has_key(key):
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19 uniqintv[key] = uniqintv[key] + 1
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20 else:
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21 uniqintv[key] = 1
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22 data[key] = flds
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23 f.close()
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24 for key in uniqintv.keys():
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25 print '\t'.join(data[key]+[str(uniqintv[key])])
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26 #flds = key.split('\t')
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27 #print '\t'.join([flds[0],flds[1],flds[2],'.',str(uniqintv[key]),flds[3]])
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28
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29 def collapseInterval(filename):
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30 uniqintv = {}
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31 data = {}
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32 f = open(filename)
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33 header = f.readline()
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34 if 'chr' in header:
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35 flds = header.strip().split('\t')
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36 key = '\t'.join([flds[0],flds[1],flds[2]])
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37 uniqintv[key] = 1
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38 data[key] = flds
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39 for line in f:
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40 flds = line.strip().split('\t')
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41 key = '\t'.join([flds[0],flds[1],flds[2]])
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42 if uniqintv.has_key(key):
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43 uniqintv[key] = uniqintv[key] + 1
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44 else:
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45 uniqintv[key] = 1
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46 data[key] = flds
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47 f.close()
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48 for key in uniqintv.keys():
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49 print '\t'.join(data[key]+[str(uniqintv[key])])
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50 #flds = key.split('\t')
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51 #print '\t'.join([flds[0],flds[1],flds[2],'.',str(uniqintv[key])])
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52
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53 import sys
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54
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55 if sys.argv[2] == 'strand':
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56 collapseInterval_strand(sys.argv[1])
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57 else:
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58 collapseInterval(sys.argv[1])
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