Mercurial > repos > xuebing > sharplabtool

comparison collapseTab.py @ 11:b7f1d9f8f3bc

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author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
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10:1558594a3c2e 11:b7f1d9f8f3bc
1 '''
2 collapse tabular files, with key columns, and max columns
3 '''
4
5 def collapseTab(filename,c_key,c_max):
6 # keeping rows with max value in column c_max
7 nCol = max(max(c_key),c_max)
8 c_max = c_max - 1
9 for i in range(len(c_key)):
10 c_key[i] = c_key[i] - 1
11 uniqintv = {}
12 data = {}
13 f = open(filename)
14 for line in f:
15 flds = line.strip().split('\t')
16 if len(flds) < nCol:
17 continue
18 key = ''
19 for i in c_key:
20 key = key + flds[i-1] # i is 1-based, python is 0-based
21 if not uniqintv.has_key(key):
22 uniqintv[key] = float(flds[c_max])
23 data[key] = flds
24 elif uniqintv[key] < float(flds[c_max]):
25 uniqintv[key] = float(flds[c_max])
26 data[key] = flds
27
28 f.close()
29 for key in uniqintv.keys():
30 print '\t'.join(data[key])
31
32 import sys
33
34 # convert string to number list
35 c_key = map(int,sys.argv[2].split(','))
36 c_max = int(sys.argv[3])
37 collapseTab(sys.argv[1],c_key,c_max)