def FetchPatternWithICIter(allNode,
adjMap,
minIC,
maxIC,
seqLis,
allPattern,
kmer2seqIdSet,
overallKmer2Cov,
pattern2IC,
startNode2rlt={},
ICminInterval=0.05,
enableParallel=False,
coreNm=8,
pattern2kmerSet={}):
Comm.PrintWithTime('current IC: min: %s, max: %s' % (minIC, maxIC),
isLogging=True)
# build the backpack model
bp = Backpack(adjMap, minIC, maxIC, seqLis, kmer2seqIdSet, overallKmer2Cov,
pattern2IC, pattern2kmerSet)
# give different start node in case that there are multiple motif
patternSet = set()
ICLis = []
if not enableParallel:
for startNode in allNode:
includedNodes = {startNode}
availNodes = adjMap[startNode]
disableNode = set()
userCov, curPattern = startNode2rlt[
startNode] if startNode in startNode2rlt and minIC <= startNode2rlt[
startNode][0] <= maxIC else bp.searchPattern(
includedNodes, availNodes, disableNode)
startNode2rlt[startNode] = (userCov, curPattern)
# INFO('current starting node: %s, current pattern: %s' % (startNode, curPattern))
if not curPattern: continue
# filter 'ACGU' and 'X[ACGU]X'
parsedPatternLis = BioinfoComm.parsePatternStr(curPattern)
charCntLis = map(lambda x: len(x), parsedPatternLis)
if set(charCntLis) == {1} or 4 in charCntLis: continue
# ==== TODO
# kmerLis = BioinfoComm.FetchAllKmerFromPattern(curPattern)
# patternLen = len(kmerLis[0])
# if patternLen == 4:
# if patternLen == 6:
# curPattern = '[GT]G[ACG][CG]'
# curPattern = '[CGT]CC[AGT]'
# curPattern = '[AGT][AGT][AGT][ACG][AT][CG]'
# ====
# calculate new information content
curIC, bp.pattern2IC = FetchPatternWeighedIC(
curPattern, bp.pattern2IC, overallKmer2Cov)
ICLis.append(curIC)
patternSet.add(curPattern)
else:
startNodeInfoLis = Parallel(n_jobs=coreNm)(delayed(
ParallelDiffStartnode)(startNode, bp, adjMap, startNode2rlt, minIC,
maxIC, overallKmer2Cov)
for startNode in allNode)
for startNode, curIC, curPattern, userCov, curPattern2IC in startNodeInfoLis:
if curIC == -1: continue
pattern2IC = dict(pattern2IC, **curPattern2IC)
startNode2rlt[startNode] = (userCov, curPattern)
ICLis.append(curIC)
patternSet.add(curPattern)
kmer2seqIdSet = bp.kmer2seqIdSet
pattern2kmerSet = bp.pattern2kmerSet
# pattern2IC = bp.pattern2IC
if not patternSet:
return allPattern, kmer2seqIdSet, pattern2IC, pattern2kmerSet # in case there is no result
allPattern = allPattern | patternSet
nextIC = min(ICLis)
# the left part
minIC1 = minIC
maxIC1 = min(nextIC, maxIC - 0.05) # at least move the bound for 0.05
if maxIC1 < maxIC and maxIC1 - minIC1 > ICminInterval:
allPattern, kmer2seqIdSet, pattern2IC, pattern2kmerSet = FetchPatternWithICIter(
allNode,
adjMap,
minIC1,
maxIC1,
seqLis,
allPattern,
kmer2seqIdSet,
overallKmer2Cov,
pattern2IC,
startNode2rlt,
enableParallel=enableParallel,
coreNm=coreNm,
pattern2kmerSet=pattern2kmerSet)
# the right part
minIC2 = max(nextIC, minIC + 0.05) # at least move the bound for 0.05
maxIC2 = maxIC
if minIC2 > minIC and maxIC2 - minIC2 > ICminInterval:
allPattern, kmer2seqIdSet, pattern2IC, pattern2kmerSet = FetchPatternWithICIter(
allNode,
adjMap,
minIC2,
maxIC2,
seqLis,
allPattern,
kmer2seqIdSet,
overallKmer2Cov,
pattern2IC,
startNode2rlt,
enableParallel=enableParallel,
coreNm=coreNm,
pattern2kmerSet=pattern2kmerSet)
INFO('iteration for IC [%s, %s]' % (minIC, maxIC))
return allPattern, kmer2seqIdSet, pattern2IC, pattern2kmerSet
