def mainFlow(folderName, mummerLink, inputContigsFilename, inputReadsFilename, useSpades, noAlignment, scoreListOutputName, outputContigsFilename, mScoreThres, conScoreThres, setCoverOption):
outputHeader, splitNum, parallelNum = "readToContigHeader", 20, 20
contigsFilename, readsFilename= "tmp" + inputContigsFilename , "tmp" + inputReadsFilename
targetToSourceContigsNamesDic = houseKeeperLib.transformFileHeaders(folderName, inputContigsFilename, contigsFilename, noAlignment)
targetToSourceReadsNamesDic = houseKeeperLib.transformFileHeaders(folderName, inputReadsFilename, readsFilename, noAlignment)
dataList = alignmentLib.extractRead2Contig(folderName, mummerLink, readsFilename, contigsFilename, splitNum, outputHeader, parallelNum, noAlignment )
connectingReadsList = readConnectivityLib.findConnectingReadsList(dataList)
spanReadsList, contigGapReadLookUpDic = readConnectivityLib.findSpanReadsList(connectingReadsList)
contigsNamesList = alignmentLib.findContigsNames(folderName, contigsFilename)
G = graphLib.formContigGraph(spanReadsList, contigsNamesList)
condenseCandidatesList = G.findCondenseCandidatesList()
multiplicityDic = G.findEdgeMultiplicity()
potentialMergesList = setCoverLib.extendConnectivityFromReads(condenseCandidatesList, connectingReadsList, contigsNamesList, setCoverOption, multiplicityDic)
if useSpades == True:
cTestLib.assignCoverageFromHeader(G, folderName, contigsFilename, targetToSourceContigsNamesDic)
else:
cTestLib.assignCoverageFromDataList(G, dataList,folderName, contigsFilename)
scoreStructList = cTestLib.calculateConfidenceScore(G, potentialMergesList)
scoreListWithDummy, dummyNodeDataRobot = setCoverLib.assignRepeatedNodesToDummy(scoreStructList)
rankingLib.rankAndMerge(folderName,contigsNamesList, contigsFilename, readsFilename, scoreListWithDummy, contigGapReadLookUpDic, mScoreThres, conScoreThres, scoreListOutputName, outputContigsFilename, dummyNodeDataRobot)
def test_findSpanReadsListEmbed(self):
connectingReadsList = []
contigDummyLRecord = [601, 800, 1, 200, 200, 200, 100.0, 800, 400, "ContigDummyL", "ReadDummy"]
contigDummyBRecord1 = [1, 200, 101, 300, 200, 200, 100.0, 200, 400, "ContigDummyB1", "ReadDummy"]
contigDummyBRecord2 = [1, 200, 350, 151, 200, 200, 100.0, 200, 400, "ContigDummyB2", "ReadDummy"]
contigDummyRRecord = [1, 200, 201, 400, 200, 200, 100.0, 800, 400, "ContigDummyR", "ReadDummy"]
connectingReadsList.append(["ReadDummy", "L", "ContigDummyL", contigDummyLRecord])
connectingReadsList.append(["ReadDummy", "B", "ContigDummyB1", contigDummyBRecord1])
connectingReadsList.append(["ReadDummy", "B", "ContigDummyB2", contigDummyBRecord2])
connectingReadsList.append(["ReadDummy", "R", "ContigDummyR", contigDummyRRecord])
spanReadsList, contigGapReadLookUpDic = readConnectivityLib.findSpanReadsList(connectingReadsList)
expectedSpanReadsList = [
["ContigDummyL_p", "ContigDummyB1_p", "ReadDummy"],
["ContigDummyB1_p", "ContigDummyB2_d", "ReadDummy"],
["ContigDummyB2_d", "ContigDummyR_p", "ReadDummy"],
]
assert spanReadsList.sort() == expectedSpanReadsList.sort()
assert len(contigGapReadLookUpDic) == 3
assert (
contigGapReadLookUpDic["ContigDummyL_p-ContigDummyB1_p"].sort()
== [[contigDummyLRecord, contigDummyBRecord1]].sort()
)
assert (
contigGapReadLookUpDic["ContigDummyB1_p-ContigDummyB2_d"].sort()
== [[contigDummyBRecord1, contigDummyBRecord2]].sort()
)
assert (
contigGapReadLookUpDic["ContigDummyB2_d-ContigDummyR_p"].sort()
== [[contigDummyBRecord2, contigDummyRRecord]].sort()
)
def test_findSpanReadsList(self):
connectingReadsList = []
contigDummyLRecord, contigDummyRRecord = [601, 800, 1, 200, 200, 200, 100.0, 800, 400, 'ContigDummyL', 'ReadDummy'], [1, 200, 201, 400, 200, 200, 100.0, 800, 400, 'ContigDummyR', 'ReadDummy']
connectingReadsList.append(['ReadDummy', 'L', 'ContigDummyL', contigDummyLRecord])
connectingReadsList.append(['ReadDummy', 'R', 'ContigDummyR', contigDummyRRecord])
spanReadsList, contigGapReadLookUpDic = readConnectivityLib.findSpanReadsList(connectingReadsList)
assert(spanReadsList == [ ['ContigDummyL_p', 'ContigDummyR_p', 'ReadDummy'] ] )
assert(len(contigGapReadLookUpDic) == 1)
assert(contigGapReadLookUpDic['ContigDummyL_p-ContigDummyR_p'].sort() == [[contigDummyLRecord,contigDummyRRecord]].sort())
def mainFlow(folderName, mummerLink, inputContigsFilename, inputReadsFilename,
useSpades, noAlignment, scoreListOutputName,
outputContigsFilename, mScoreThres, conScoreThres,
setCoverOption):
outputHeader, splitNum, parallelNum = "readToContigHeader", 20, 20
contigsFilename, readsFilename = "tmp" + inputContigsFilename, "tmp" + inputReadsFilename
targetToSourceContigsNamesDic = houseKeeperLib.transformFileHeaders(
folderName, inputContigsFilename, contigsFilename, noAlignment)
targetToSourceReadsNamesDic = houseKeeperLib.transformFileHeaders(
folderName, inputReadsFilename, readsFilename, noAlignment)
dataList = alignmentLib.extractRead2Contig(folderName, mummerLink,
readsFilename, contigsFilename,
splitNum, outputHeader,
parallelNum, noAlignment)
connectingReadsList = readConnectivityLib.findConnectingReadsList(dataList)
spanReadsList, contigGapReadLookUpDic = readConnectivityLib.findSpanReadsList(
connectingReadsList)
contigsNamesList = alignmentLib.findContigsNames(folderName,
contigsFilename)
G = graphLib.formContigGraph(spanReadsList, contigsNamesList)
condenseCandidatesList = G.findCondenseCandidatesList()
multiplicityDic = G.findEdgeMultiplicity()
potentialMergesList = setCoverLib.extendConnectivityFromReads(
condenseCandidatesList, connectingReadsList, contigsNamesList,
setCoverOption, multiplicityDic)
if useSpades == True:
cTestLib.assignCoverageFromHeader(G, folderName, contigsFilename,
targetToSourceContigsNamesDic)
else:
cTestLib.assignCoverageFromDataList(G, dataList, folderName,
contigsFilename)
scoreStructList = cTestLib.calculateConfidenceScore(G, potentialMergesList)
scoreListWithDummy, dummyNodeDataRobot = setCoverLib.assignRepeatedNodesToDummy(
scoreStructList)
rankingLib.rankAndMerge(folderName, contigsNamesList, contigsFilename,
readsFilename, scoreListWithDummy,
contigGapReadLookUpDic, mScoreThres, conScoreThres,
scoreListOutputName, outputContigsFilename,
dummyNodeDataRobot)
def test_findSpanReadsList(self):
connectingReadsList = []
contigDummyLRecord, contigDummyRRecord = (
[601, 800, 1, 200, 200, 200, 100.0, 800, 400, "ContigDummyL", "ReadDummy"],
[1, 200, 201, 400, 200, 200, 100.0, 800, 400, "ContigDummyR", "ReadDummy"],
)
connectingReadsList.append(["ReadDummy", "L", "ContigDummyL", contigDummyLRecord])
connectingReadsList.append(["ReadDummy", "R", "ContigDummyR", contigDummyRRecord])
spanReadsList, contigGapReadLookUpDic = readConnectivityLib.findSpanReadsList(connectingReadsList)
assert spanReadsList == [["ContigDummyL_p", "ContigDummyR_p", "ReadDummy"]]
assert len(contigGapReadLookUpDic) == 1
assert (
contigGapReadLookUpDic["ContigDummyL_p-ContigDummyR_p"].sort()
== [[contigDummyLRecord, contigDummyRRecord]].sort()
)
def test_findSpanReadsListEmbed(self):
connectingReadsList = []
contigDummyLRecord = [601, 800, 1, 200, 200, 200, 100.0, 800, 400, 'ContigDummyL', 'ReadDummy']
contigDummyBRecord1 = [1, 200, 101, 300, 200, 200, 100.0, 200, 400, 'ContigDummyB1', 'ReadDummy']
contigDummyBRecord2 = [1, 200, 350, 151, 200, 200, 100.0, 200, 400, 'ContigDummyB2', 'ReadDummy']
contigDummyRRecord = [1, 200, 201, 400, 200, 200, 100.0, 800, 400, 'ContigDummyR', 'ReadDummy']
connectingReadsList.append(['ReadDummy', 'L', 'ContigDummyL', contigDummyLRecord])
connectingReadsList.append(['ReadDummy', 'B', 'ContigDummyB1', contigDummyBRecord1])
connectingReadsList.append(['ReadDummy', 'B', 'ContigDummyB2', contigDummyBRecord2])
connectingReadsList.append(['ReadDummy', 'R', 'ContigDummyR', contigDummyRRecord])
spanReadsList, contigGapReadLookUpDic = readConnectivityLib.findSpanReadsList(connectingReadsList)
expectedSpanReadsList = [['ContigDummyL_p', 'ContigDummyB1_p', 'ReadDummy'], \
['ContigDummyB1_p', 'ContigDummyB2_d', 'ReadDummy'], \
['ContigDummyB2_d', 'ContigDummyR_p', 'ReadDummy']]
assert(spanReadsList.sort() == expectedSpanReadsList.sort())
assert(len(contigGapReadLookUpDic) == 3)
assert(contigGapReadLookUpDic['ContigDummyL_p-ContigDummyB1_p'].sort() == [[contigDummyLRecord,contigDummyBRecord1]].sort())
assert(contigGapReadLookUpDic['ContigDummyB1_p-ContigDummyB2_d'].sort() == [[contigDummyBRecord1,contigDummyBRecord2]].sort())
assert(contigGapReadLookUpDic['ContigDummyB2_d-ContigDummyR_p'].sort() == [[contigDummyBRecord2,contigDummyRRecord]].sort())