Mercurial > repos > xuebing > sharplabtool
comparison tools/mytools/collapseBed2.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 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) |