def FetchPatternCov(curPattern, seqLis, kmer2seqIdInt):
"""
fetch the sequences ID in seqLis that curPattern covers
***
to speed up
1. check whether current has already be calculated
2. parse pattern into kmer and store seq id in kmer2seqIdLis
***
"""
seqCnt = len(seqLis)
if curPattern in kmer2seqIdInt:
patternCovSeqIdxInt = kmer2seqIdInt[curPattern]
else:
allCovIdLis = []
kmerLis = FetchAllKmerFromPattern(curPattern)
for kmer in kmerLis:
if kmer in kmer2seqIdInt:
allCovIdLis.append(kmer2seqIdInt[kmer])
else:
kmerCovIdxSet = {seqId for seqId, seq in enumerate(seqLis) if kmer in seq}
kmerCovIdxBitarray = IdxLis2bin(kmerCovIdxSet, seqCnt)
kmerCovIdxInt = Comm.bitarray2int(kmerCovIdxBitarray)
kmer2seqIdInt[kmer] = kmerCovIdxInt
allCovIdLis.append(kmerCovIdxInt)
patternCovSeqIdxInt = reduce(lambda x, y: x | y, allCovIdLis)
kmer2seqIdInt[curPattern] = patternCovSeqIdxInt
cov = covIdxInt2covCnt(patternCovSeqIdxInt)
return cov, patternCovSeqIdxInt, kmer2seqIdInt
def formatCovId(kmer2seqIdSet, totalSeqCnt):
"""
format covered sequences Id set into binary num
"""
userKmer2seqIdInt = {}
for kmer, seqIdxSet in kmer2seqIdSet.iteritems():
covIdxBitArray = IdxLis2bin(seqIdxSet, totalSeqCnt)
covIdxBitInt = Comm.bitarray2int(covIdxBitArray)
userKmer2seqIdInt[kmer] = covIdxBitInt
return userKmer2seqIdInt
def FetchCovSeqDetail(seqMatrix, kmer, samplingSize):
"""
fetch sequence id in seqMatrix covered by kmer
"""
covIdxMatrix = []
covLis = []
for seqLis in seqMatrix:
covIdxLis = {seqId for seqId, seq in enumerate(seqLis) if kmer in seq}
covIdxBitarray = BioinfoComm.IdxLis2bin(covIdxLis, samplingSize)
covIdxInt = Comm.bitarray2int(covIdxBitarray)
covIdxMatrix.append(covIdxInt)
covLis.append(int(bitarray.bitarray.count(covIdxBitarray)))
# to save memory
covIdxMatrix = np.array(covIdxMatrix)
return covIdxMatrix, covLis
