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11
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1 '''
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2 collapse tabular files, with key columns, and max columns
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3 '''
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4
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5 def collapseTab(filename,c_key,c_max):
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6 # keeping rows with max value in column c_max
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7 nCol = max(max(c_key),c_max)
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8 c_max = c_max - 1
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9 for i in range(len(c_key)):
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10 c_key[i] = c_key[i] - 1
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11 uniqintv = {}
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12 data = {}
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13 f = open(filename)
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14 for line in f:
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15 flds = line.strip().split('\t')
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16 if len(flds) < nCol:
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17 continue
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18 key = ''
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19 for i in c_key:
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20 key = key + flds[i-1] # i is 1-based, python is 0-based
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21 if not uniqintv.has_key(key):
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22 uniqintv[key] = float(flds[c_max])
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23 data[key] = flds
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24 elif uniqintv[key] < float(flds[c_max]):
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25 uniqintv[key] = float(flds[c_max])
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26 data[key] = flds
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27
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28 f.close()
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29 for key in uniqintv.keys():
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30 print '\t'.join(data[key])
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31
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32 import sys
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33
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34 # convert string to number list
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35 c_key = map(int,sys.argv[2].split(','))
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36 c_max = int(sys.argv[3])
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37 collapseTab(sys.argv[1],c_key,c_max)
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