def testEcoliGenome(self): def encode(seq): return [(len(list(group)), name) for name, group in groupby(seq)] with open('data/burrow/ecoligenome.txt') as fp: sequence = fp.readline().strip() print "Transform" bwt = burrowWheelerTransform(sequence) print "Start Encoding" encoded = encode(bwt) # print encoded print len([(x, y) for x, y in encoded if x >= 10])
def testEcoliGenome(self): def encode(seq): return [(len(list(group)), name) for name, group in groupby(seq)] with open('data/burrow/ecoligenome.txt') as fp: sequence = fp.readline().strip() print "Transform" bwt = burrowWheelerTransform(sequence) print "Start Encoding" encoded = encode(bwt) # print encoded print len([(x, y) for x, y in encoded if x >= 10 ])
def testBurrowWheelerTransform2(self): print burrowWheelerTransform('GATTGCTTTT$')
def testBurrowWheelerTransform(self): with open('data/burrow/transform.txt') as fp: sequences = [x.strip() for x in fp.readlines()] print burrowWheelerTransform(sequences[0])