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comparison collapseBed2.py @ 14:76e1b1b21cce default tip

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author xuebing
date Tue, 13 Mar 2012 19:05:10 -0400
parents 292186c14b08
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13:292186c14b08 14:76e1b1b21cce
1 '''
2 collapse intervals
3 '''
4
5 def collapseInterval_strand(filename,c_strand,c_score):
6 # keeping max column c
7 uniqintv = {}
8 data = {}
9 f = open(filename)
10 header = f.readline()
11 if 'chr' in header:
12 flds = header.strip().split('\t')
13 key = '\t'.join([flds[0],flds[1],flds[2],flds[c_strand]])
14 uniqintv[key] = float(flds[c_score])
15 data[key] = flds
16 for line in f:
17 flds = line.strip().split('\t')
18 key = '\t'.join([flds[0],flds[1],flds[2],flds[c_strand]])
19 if not uniqintv.has_key(key):
20 uniqintv[key] = float(flds[c_score])
21 data[key] = flds
22 elif uniqintv[key] < float(flds[c_score]):
23 uniqintv[key] = float(flds[c_score])
24 data[key] = flds
25
26 f.close()
27 for key in uniqintv.keys():
28 print '\t'.join(data[key])
29
30 import sys
31
32 if sys.argv[2] == '0':#ignore strand
33 sys.argv[2] = 1
34 if sys.argv[3] == '0':# ignore score
35 sys.argv[3] = 2
36 collapseInterval_strand(sys.argv[1],int(sys.argv[2])-1,int(sys.argv[3])-1)