Mercurial > repos > xuebing > sharplabtool
view tools/mytools/collapseBed2.py @ 0:9071e359b9a3
Uploaded
author | xuebing |
---|---|
date | Fri, 09 Mar 2012 19:37:19 -0500 |
parents | |
children |
line wrap: on
line source
''' collapse intervals ''' def collapseInterval_strand(filename,c_strand,c_score): # keeping max column c uniqintv = {} data = {} f = open(filename) header = f.readline() if 'chr' in header: flds = header.strip().split('\t') key = '\t'.join([flds[0],flds[1],flds[2],flds[c_strand]]) uniqintv[key] = float(flds[c_score]) data[key] = flds for line in f: flds = line.strip().split('\t') key = '\t'.join([flds[0],flds[1],flds[2],flds[c_strand]]) if not uniqintv.has_key(key): uniqintv[key] = float(flds[c_score]) data[key] = flds elif uniqintv[key] < float(flds[c_score]): uniqintv[key] = float(flds[c_score]) data[key] = flds f.close() for key in uniqintv.keys(): print '\t'.join(data[key]) import sys if sys.argv[2] == '0':#ignore strand sys.argv[2] = 1 if sys.argv[3] == '0':# ignore score sys.argv[3] = 2 collapseInterval_strand(sys.argv[1],int(sys.argv[2])-1,int(sys.argv[3])-1)