Mercurial > repos > xuebing > sharplabtool
diff bedClean.py @ 14:76e1b1b21cce default tip
Deleted selected files
author | xuebing |
---|---|
date | Tue, 13 Mar 2012 19:05:10 -0400 |
parents | 292186c14b08 |
children |
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--- a/bedClean.py Sat Mar 10 08:17:36 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -import sys - -def readChrSize(filename): - f = open(filename) - chrSize = {} - for line in f: - chrom,size = line.strip().split() - chrSize[chrom]=int(size) - f.close() - return chrSize - -def cleanFile(filename,chrSize,outfile): - f = open(filename) - out = open(outfile,'w') - i = 0 - for line in f: - i = i + 1 - flds = line.strip().split('\t') - if len(flds) < 3: - print 'line',i,'incomplete line:\n',line - elif chrSize.has_key(flds[0]): - if int(flds[1]) > int(flds[2]): - tmp = flds[1] - flds[1] = flds[2] - flds[2] = tmp - if int( flds[1]) < 0 or int(flds[2]) <0: - print 'line',i,'negative coordinates:\n',line - elif int(flds[2]) > chrSize[flds[0]]: - print 'line',i,'end larger than chr size:\n',line - else: - out.write('\t'.join(flds)+'\n') - else: - print 'line',i,'chromosome',flds[0],'not found!\n',line - f.close() - out.close() - -cleanFile(sys.argv[1],readChrSize(sys.argv[2]),sys.argv[3])