11 print 'psyco not running'
13 from cistematic.genomes import Genome
19 print "getmers: version 1.2"
22 print 'usage: python %s genome merlen chrAny:start-stop outfile' % argv[0]
30 getmers(genome, merlen, location, outfilename)
33 def getmers(genome, merlen, location, outfilename):
34 (chrom, pos) = location.split(':')
36 (start, stop) = pos.split('-')
38 regionlength = int(stop) - start + 1
42 seq = hg.sequence(chrom, start, regionlength)
44 outfile = open(outfilename,'w')
45 print 'writing %d %d-mers' % (regionlength - merlen, merlen)
46 for index in range(regionlength - merlen):
47 outfile.write(seq[index:index + merlen].upper() + '\n')
51 if __name__ == "__main__":