def multiPatternMatching(sequence, patterns):
bwt = burrowWheelerTransform(sequence)
suffixArray = buildSuffixArray(sequence)
for match in findPatterns(bwt, patterns):
for pos in match:
yield suffixArray[pos]
def multiPatternMatching(sequence, patterns):
bwt = burrowWheelerTransform(sequence)
suffixArray = buildSuffixArray(sequence)
for match in findPatterns(bwt, patterns):
for pos in match:
yield suffixArray[pos]
def patternMatchWithMismatches(sequence, patterns, maxMismatches):
"""
Find locations of Patterns in the Sequence which have <= No of Mismatches
"""
bwt = burrowWheelerTransform(sequence)
suffixArray = buildSuffixArray(sequence)
_, lastToFirst = firstLast(bwt)
for pattern in patterns:
fragmentIndexes = list(findSeedPositions2(bwt, lastToFirst, pattern, maxMismatches))
candidatePos = Counter([suffixArray[y] - offset for offset, x in fragmentIndexes for y in x])
seedPositions = [cp[0] for cp in takewhile(lambda x : x[1] > 1, candidatePos.most_common())]
for pos in seedPositions:
if isSimilar(sequence[pos:pos + len(pattern)], pattern, maxMismatches):
yield pos
def patternMatchWithMismatches(sequence, patterns, maxMismatches):
"""
Find locations of Patterns in the Sequence which have <= No of Mismatches
"""
bwt = burrowWheelerTransform(sequence)
suffixArray = buildSuffixArray(sequence)
_, lastToFirst = firstLast(bwt)
for pattern in patterns:
fragmentIndexes = list(
findSeedPositions2(bwt, lastToFirst, pattern, maxMismatches))
candidatePos = Counter([
suffixArray[y] - offset for offset, x in fragmentIndexes for y in x
])
seedPositions = [
cp[0]
for cp in takewhile(lambda x: x[1] > 1, candidatePos.most_common())
]
for pos in seedPositions:
if isSimilar(sequence[pos:pos + len(pattern)], pattern,
maxMismatches):
yield pos
def partialSuffixArray(sequence, freq):
return [ (i, v) for i, v in enumerate(buildSuffixArray(sequence)) if v % freq == 0 ]
def testBuildSuffixArray(self):
with open('data/suffix/buildsuffixarray.txt') as fp:
with open('data/suffix/buildsuffixarray.out', 'w') as output:
sequences = [x.strip() for x in fp.readlines()]
print ', '.join([str(x) for x in buildSuffixArray(sequences[0])])
def partialSuffixArray(sequence, freq):
return [(i, v) for i, v in enumerate(buildSuffixArray(sequence))
if v % freq == 0]
def testBuildSuffixArray(self):
with open('data/suffix/buildsuffixarray.txt') as fp:
with open('data/suffix/buildsuffixarray.out', 'w') as output:
sequences = [x.strip() for x in fp.readlines()]
print ', '.join(
[str(x) for x in buildSuffixArray(sequences[0])])
