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$')
def testBurrowWheelerTransform(self):
with open('data/burrow/transform.txt') as fp:
sequences = [x.strip() for x in fp.readlines()]
print burrowWheelerTransform(sequences[0])
def testBurrowWheelerTransform2(self):
print burrowWheelerTransform('GATTGCTTTT$')
def testBurrowWheelerTransform(self):
with open('data/burrow/transform.txt') as fp:
sequences = [x.strip() for x in fp.readlines()]
print burrowWheelerTransform(sequences[0])