def removeRedundantRefvsQuery(folderName, mummerLink, fileR, fileQ, outputFileName):
thres = 10
if True:
alignerRobot.useMummerAlignBatch(
mummerLink, folderName, [["redundantRvsQ", fileR, fileQ, ""]], houseKeeper.globalParallel
)
dataList = alignerRobot.extractMumData(folderName, "redundantRvsQOut")
lenDicR = IORobot.obtainLength(folderName, fileR)
lenDicQ = IORobot.obtainLength(folderName, fileQ)
isRedundantList = []
for eachitem in dataList:
match1, match2, name1, name2 = eachitem[4], eachitem[5], eachitem[7], eachitem[8]
l1, l2 = lenDicR[name1], lenDicQ[name2]
if abs(l2 - match2) < thres:
isRedundantList.append(name2)
# print lenDicQ
nonRedundantList = obtainComplement(lenDicQ, isRedundantList)
print nonRedundantList
IORobot.putListToFileO(folderName, fileQ, outputFileName, nonRedundantList)
os.system("cp " + folderName + "SC_n_tmp.fasta " + folderName + "SC_n.fasta")
def removeEmbedded(folderName , mummerLink):
print "removeEmbedded"
thres = 10
os.system("sed -e 's/|//g' " + folderName + "contigs.fasta > " + folderName + "contigs2.fasta")
os.system("cp " + folderName + "contigs2.fasta " + folderName + "contigs.fasta")
if not os.path.isfile(folderName + "selfOut"):
alignerRobot.useMummerAlignBatch(mummerLink, folderName, [["self", "contigs.fasta", "contigs.fasta", ""]], houseKeeper.globalParallel )
# alignerRobot.useMummerAlign(mummerLink, folderName, "self", "contigs.fasta", "contigs.fasta")
# outputName, referenceName, queryName, specialName
lenDic = IORobot.obtainLength(folderName, 'contigs.fasta')
removeList = alignerRobot.extractMumDataAndRemove(folderName,"selfOut",lenDic,thres)
nameList = []
for eachitem in lenDic:
nameList.append(eachitem)
print len(nameList)
for eachitem in removeList:
if eachitem in nameList:
nameList.remove(eachitem)
print len(nameList)
IORobot.putListToFileO(folderName, "contigs.fasta", "noEmbed", nameList)
def removeRedundantRefvsQuery(folderName, mummerLink, fileR, fileQ,
outputFileName):
thres = 10
if True:
alignerRobot.useMummerAlignBatch(mummerLink, folderName,
[["redundantRvsQ", fileR, fileQ, ""]],
houseKeeper.globalParallel)
dataList = alignerRobot.extractMumData(folderName, "redundantRvsQOut")
lenDicR = IORobot.obtainLength(folderName, fileR)
lenDicQ = IORobot.obtainLength(folderName, fileQ)
isRedundantList = []
for eachitem in dataList:
match1, match2, name1, name2 = eachitem[4], eachitem[5], eachitem[
7], eachitem[8]
l1, l2 = lenDicR[name1], lenDicQ[name2]
if abs(l2 - match2) < thres:
isRedundantList.append(name2)
#print lenDicQ
nonRedundantList = obtainComplement(lenDicQ, isRedundantList)
print nonRedundantList
IORobot.putListToFileO(folderName, fileQ, outputFileName, nonRedundantList)
os.system("cp " + folderName + "SC_n_tmp.fasta " + folderName +
"SC_n.fasta")
def removeRedundantWithFile(folderName, mummerLink, inputFilename,
mummerTmpName, outputFileName):
thres = 10
os.system("sed -e 's/|//g' " + folderName + inputFilename + ".fasta > " +
folderName + inputFilename + "2.fasta")
os.system("cp " + folderName + inputFilename + "2.fasta " + folderName +
inputFilename + ".fasta")
if True:
alignerRobot.useMummerAlignBatch(mummerLink, folderName, [[
mummerTmpName, inputFilename + ".fasta", inputFilename + ".fasta",
""
]], houseKeeper.globalParallel)
# alignerRobot.useMummerAlign(mummerLink, folderName, "self", "contigs.fasta", "contigs.fasta")
# outputName, referenceName, queryName, specialName
dataList = alignerRobot.extractMumData(folderName, mummerTmpName + "Out")
dataList = alignerRobot.transformCoor(dataList)
lenDic = IORobot.obtainLength(folderName, inputFilename + '.fasta')
removeList = []
shortEmbedClusterDic = {}
for eachitem in lenDic:
shortEmbedClusterDic[eachitem] = clusterElem(eachitem)
for eachitem in dataList:
match1, match2, name1, name2 = eachitem[4], eachitem[5], eachitem[
7], eachitem[8]
if name1 != name2:
l1, l2 = lenDic[name1], lenDic[name2]
if abs(l1 - match1) < thres and abs(l2 - match2) > thres:
removeList.append(name1)
elif abs(l1 - match1) > thres and abs(l2 - match2) < thres:
removeList.append(name2)
elif abs(l1 - match1) < thres and abs(l2 - match2) < thres:
print "Both shortembedd", eachitem
union(shortEmbedClusterDic[name1], shortEmbedClusterDic[name2])
nameList = obtainComplement(lenDic, removeList)
returnList = []
for eachitem in nameList:
if find(shortEmbedClusterDic[eachitem]).id == eachitem:
returnList.append(eachitem)
print "len(nameList), len(returnList)", len(nameList), len(returnList)
IORobot.putListToFileO(folderName, inputFilename + ".fasta",
outputFileName, returnList)
def removeRedundantWithFile(folderName, mummerLink, inputFilename, mummerTmpName, outputFileName):
thres = 10
os.system("sed -e 's/|//g' " + folderName + inputFilename + ".fasta > " + folderName + inputFilename + "2.fasta")
os.system("cp " + folderName + inputFilename + "2.fasta " + folderName + inputFilename + ".fasta")
if True:
alignerRobot.useMummerAlignBatch(
mummerLink,
folderName,
[[mummerTmpName, inputFilename + ".fasta", inputFilename + ".fasta", ""]],
houseKeeper.globalParallel,
)
# alignerRobot.useMummerAlign(mummerLink, folderName, "self", "contigs.fasta", "contigs.fasta")
# outputName, referenceName, queryName, specialName
dataList = alignerRobot.extractMumData(folderName, mummerTmpName + "Out")
dataList = alignerRobot.transformCoor(dataList)
lenDic = IORobot.obtainLength(folderName, inputFilename + ".fasta")
removeList = []
shortEmbedClusterDic = {}
for eachitem in lenDic:
shortEmbedClusterDic[eachitem] = clusterElem(eachitem)
for eachitem in dataList:
match1, match2, name1, name2 = eachitem[4], eachitem[5], eachitem[7], eachitem[8]
if name1 != name2:
l1, l2 = lenDic[name1], lenDic[name2]
if abs(l1 - match1) < thres and abs(l2 - match2) > thres:
removeList.append(name1)
elif abs(l1 - match1) > thres and abs(l2 - match2) < thres:
removeList.append(name2)
elif abs(l1 - match1) < thres and abs(l2 - match2) < thres:
print "Both shortembedd", eachitem
union(shortEmbedClusterDic[name1], shortEmbedClusterDic[name2])
nameList = obtainComplement(lenDic, removeList)
returnList = []
for eachitem in nameList:
if find(shortEmbedClusterDic[eachitem]).id == eachitem:
returnList.append(eachitem)
print "len(nameList), len(returnList)", len(nameList), len(returnList)
IORobot.putListToFileO(folderName, inputFilename + ".fasta", outputFileName, returnList)
def removeEmbedded(folderName, mummerLink):
print "removeEmbedded"
thres = 10
command = r'''perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' ''' + folderName + "raw_reads.fasta > " + folderName + houseKeeper.globalReadName
os.system(command)
command = r'''perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' ''' + folderName + "contigs.fasta > " + folderName + houseKeeper.globalContigName
os.system(command)
if True:
alignerRobot.useMummerAlignBatch(mummerLink, folderName, [[
"self", houseKeeper.globalContigName, houseKeeper.globalContigName,
""
]], houseKeeper.globalParallel)
# alignerRobot.useMummerAlign(mummerLink, folderName, "self", "contigs.fasta", "contigs.fasta")
# outputName, referenceName, queryName, specialName
dataList = alignerRobot.extractMumData(folderName, "selfOut")
dataList = alignerRobot.transformCoor(dataList)
lenDic = IORobot.obtainLength(folderName, houseKeeper.globalContigName)
removeList = []
for eachitem in dataList:
match1, match2, name1, name2 = eachitem[4], eachitem[5], eachitem[
7], eachitem[8]
if name1 != name2:
l1, l2 = lenDic[name1], lenDic[name2]
if abs(l1 - match1) < thres and abs(l2 - match2) > thres:
removeList.append(name1)
elif abs(l1 - match1) > thres and abs(l2 - match2) < thres:
removeList.append(name2)
elif abs(l1 - match1) < thres and abs(l2 - match2) < thres:
print "Both shortembedd", eachitem
nameList = []
for eachitem in lenDic:
nameList.append(eachitem)
print len(nameList)
for eachitem in removeList:
if eachitem in nameList:
nameList.remove(eachitem)
print len(nameList)
IORobot.putListToFileO(folderName, houseKeeper.globalContigName, "noEmbed",
nameList)
def removeEmbedded(folderName, mummerLink):
print "removeEmbedded"
thres = 10
os.system("sed -e 's/|//g' " + folderName + "contigs.fasta > " +
folderName + "contigs2.fasta")
os.system("cp " + folderName + "contigs2.fasta " + folderName +
"contigs.fasta")
if True:
print "removeEmbedded: Aligning contigs.fasta to contigs.fasta, outputs are self*.delta"
alignerRobot.useMummerAlignBatch(
mummerLink, folderName,
[["self", "contigs.fasta", "contigs.fasta", ""]],
houseKeeper.globalParallel)
# alignerRobot.useMummerAlign(mummerLink, folderName, "self", "contigs.fasta", "contigs.fasta")
# outputName, referenceName, queryName, specialName
print "removeEmbedded: Extracting MUMmer data from delta files to selfOut"
dataList = alignerRobot.extractMumData(folderName, "selfOut")
dataList = alignerRobot.transformCoor(dataList)
lenDic = IORobot.obtainLength(folderName, 'contigs.fasta')
removeList = []
for eachitem in dataList:
match1, match2, name1, name2 = eachitem[4], eachitem[5], eachitem[
7], eachitem[8]
if name1 != name2:
l1, l2 = lenDic[name1], lenDic[name2]
if abs(l1 - match1) < thres and abs(l2 - match2) > thres:
removeList.append(name1)
elif abs(l1 - match1) > thres and abs(l2 - match2) < thres:
removeList.append(name2)
elif abs(l1 - match1) < thres and abs(l2 - match2) < thres:
print "Both shortembedd", eachitem
nameList = []
for eachitem in lenDic:
nameList.append(eachitem)
print len(nameList)
for eachitem in removeList:
if eachitem in nameList:
nameList.remove(eachitem)
print len(nameList)
print "removeEmbedded: Outputting non-contained contigs to noEmbed.fasta"
IORobot.putListToFileO(folderName, "contigs.fasta", "noEmbed", nameList)
def removeEmbedded(folderName , mummerLink):
print "removeEmbedded"
thres = 10
command= r'''perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' ''' + folderName + "raw_reads.fasta > " + folderName + houseKeeper.globalReadName
os.system(command)
command= r'''perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' ''' + folderName + "contigs.fasta > " + folderName + houseKeeper.globalContigName
os.system(command)
if True:
alignerRobot.useMummerAlignBatch(mummerLink, folderName, [["self", houseKeeper.globalContigName, houseKeeper.globalContigName, ""]], houseKeeper.globalParallel)
# alignerRobot.useMummerAlign(mummerLink, folderName, "self", "contigs.fasta", "contigs.fasta")
# outputName, referenceName, queryName, specialName
dataList = alignerRobot.extractMumData(folderName, "selfOut")
dataList = alignerRobot.transformCoor(dataList)
lenDic = IORobot.obtainLength(folderName, houseKeeper.globalContigName)
removeList = []
for eachitem in dataList:
match1, match2, name1, name2 = eachitem[4], eachitem[5], eachitem[7], eachitem[8]
if name1 != name2:
l1, l2 = lenDic[name1], lenDic[name2]
if abs(l1 - match1) < thres and abs(l2 - match2) > thres:
removeList.append(name1)
elif abs(l1 - match1) > thres and abs(l2 - match2) < thres:
removeList.append(name2)
elif abs(l1 - match1) < thres and abs(l2 - match2) < thres:
print "Both shortembedd", eachitem
nameList = []
for eachitem in lenDic:
nameList.append(eachitem)
print len(nameList)
for eachitem in removeList:
if eachitem in nameList:
nameList.remove(eachitem)
print len(nameList)
IORobot.putListToFileO(folderName, houseKeeper.globalContigName, "noEmbed", nameList)
def mainFlow(folderName, mummerLink, pickupname, mapcontigsname):
print "Go Bears! ! !"
print "pickupname, mapcontigsname", pickupname, mapcontigsname
if not pickupname in [
"noEmbed.fasta", "improved.fasta", "improved2.fasta"
]:
nonRedundantResolver.removeEmbedded(folderName, mummerLink)
if not pickupname in ["improved.fasta", "improved2.fasta"]:
overlapResolver.fetchSuccessor(folderName, mummerLink)
overlapResolver.formSeqGraph(folderName, mummerLink)
if not pickupname in ["improved2.fasta"]:
gapFiller.fillGap(folderName, mummerLink)
twoRepeatOneBridgeSolver.xPhased(folderName, mummerLink)
# ECReduction(folderName , mummerLink )
# compareWithReference(folderName , mummerLink)
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName,
"noEmbedtmp.fasta", "noEmbed.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName,
"improvedtmp.fasta", "improved.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName,
"improved2tmp.fasta", "improved2.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName,
"improved3tmp.fasta", "improved3.fasta")
if mapcontigsname != None:
houseKeeper.performMapping(folderName, mummerLink, mapcontigsname)
print "<3 Do cool things that matter <3"
def mainFlow(folderName , mummerLink, pickupname, mapcontigsname):
print "Go Bears! ! !"
print "pickupname, mapcontigsname", pickupname, mapcontigsname
if not pickupname in ["noEmbed.fasta", "improved.fasta", "improved2.fasta"]:
nonRedundantResolver.removeEmbedded(folderName , mummerLink)
if not pickupname in ["improved.fasta", "improved2.fasta"]:
overlapResolver.fetchSuccessor(folderName , mummerLink)
overlapResolver.formSeqGraph(folderName , mummerLink)
if not pickupname in ["improved2.fasta"]:
gapFiller.fillGap(folderName , mummerLink)
twoRepeatOneBridgeSolver.xPhased(folderName , mummerLink)
# ECReduction(folderName , mummerLink )
# compareWithReference(folderName , mummerLink)
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "noEmbedtmp.fasta", "noEmbed.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "improvedtmp.fasta", "improved.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "improved2tmp.fasta", "improved2.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "improved3tmp.fasta", "improved3.fasta")
if mapcontigsname != None:
houseKeeper.performMapping(folderName, mummerLink, mapcontigsname)
print "<3 Do cool things that matter <3"
def removeEmbedded(folderName, mummerLink):
print "removeEmbedded"
thres = 10
os.system("sed -e 's/|//g' " + folderName + "contigs.fasta > " + folderName + "contigs2.fasta")
os.system("cp " + folderName + "contigs2.fasta " + folderName + "contigs.fasta")
if True:
print "removeEmbedded: Aligning contigs.fasta to contigs.fasta, outputs are self*.delta"
alignerRobot.useMummerAlignBatch(
mummerLink, folderName, [["self", "contigs.fasta", "contigs.fasta", ""]], houseKeeper.globalParallel
)
# alignerRobot.useMummerAlign(mummerLink, folderName, "self", "contigs.fasta", "contigs.fasta")
# outputName, referenceName, queryName, specialName
print "removeEmbedded: Extracting MUMmer data from delta files to selfOut"
dataList = alignerRobot.extractMumData(folderName, "selfOut")
dataList = alignerRobot.transformCoor(dataList)
lenDic = IORobot.obtainLength(folderName, "contigs.fasta")
removeList = []
for eachitem in dataList:
match1, match2, name1, name2 = eachitem[4], eachitem[5], eachitem[7], eachitem[8]
if name1 != name2:
l1, l2 = lenDic[name1], lenDic[name2]
if abs(l1 - match1) < thres and abs(l2 - match2) > thres:
removeList.append(name1)
elif abs(l1 - match1) > thres and abs(l2 - match2) < thres:
removeList.append(name2)
elif abs(l1 - match1) < thres and abs(l2 - match2) < thres:
print "Both shortembedd", eachitem
nameList = []
for eachitem in lenDic:
nameList.append(eachitem)
print len(nameList)
for eachitem in removeList:
if eachitem in nameList:
nameList.remove(eachitem)
print len(nameList)
print "removeEmbedded: Outputting non-contained contigs to noEmbed.fasta"
IORobot.putListToFileO(folderName, "contigs.fasta", "noEmbed", nameList)
def formSeqGraph(folderName , mummerLink):
print "formSeqGraph"
startList, graphNodes = [], []
print "formSeqGraph: Reading in best successors and predecessors"
rightConnect = readConnectList(folderName, "rightConnect.txt")
leftConnect = readConnectList(folderName, "leftConnect.txt")
numberOfNodes = len(rightConnect)
print "formSeqGraph: Initializing seqGraph"
G = graphLib.seqGraph(numberOfNodes)
print "formSeqGraph: Adding edges to seqGraph"
for eachitem, i in zip(rightConnect, range(len(rightConnect))):
index = i
connector, weight = eachitem
G.insertEdge(index, connector, weight)
for eachitem, i in zip(leftConnect, range(len(leftConnect))):
index = i
connector, weight = eachitem
G.insertEdge(connector, index, weight)
G.cleanEdge()
G.condense()
print "formSeqGraph: Outputting seqGraph to condensedGraph.txt"
G.saveToFile(folderName, "condensedGraph.txt")
G.checkSelfLoops()
G.checkCompleteness()
G2 = graphLib.seqGraph(0)
G2.loadFromFile(folderName, "condensedGraph.txt")
houseKeeper.compareGraphUnitTest(G, G2)
G.reportDummyUsefulNode()
G.reportEdge()
graphFileName = "condensedGraph.txt"
contigFile = "noEmbed_Double.fasta"
outContigFile = "improved.fasta"
outOpenList = "openZone.txt"
print "formSeqGraph: Outputting improved contigs from seqGraph to improved.fasta"
IORobot.readContigOut(folderName, mummerLink, graphFileName, contigFile, outContigFile, outOpenList)
def formSeqGraph(folderName, mummerLink):
print "formSeqGraph"
startList, graphNodes = [], []
print "formSeqGraph: Reading in best successors and predecessors"
rightConnect = readConnectList(folderName, "rightConnect.txt")
leftConnect = readConnectList(folderName, "leftConnect.txt")
numberOfNodes = len(rightConnect)
print "formSeqGraph: Initializing seqGraph"
G = graphLib.seqGraph(numberOfNodes)
print "formSeqGraph: Adding edges to seqGraph"
for eachitem, i in zip(rightConnect, range(len(rightConnect))):
index = i
connector, weight = eachitem
G.insertEdge(index, connector, weight)
for eachitem, i in zip(leftConnect, range(len(leftConnect))):
index = i
connector, weight = eachitem
G.insertEdge(connector, index, weight)
G.cleanEdge()
G.condense()
print "formSeqGraph: Outputting seqGraph to condensedGraph.txt"
G.saveToFile(folderName, "condensedGraph.txt")
G.checkSelfLoops()
G.checkCompleteness()
G2 = graphLib.seqGraph(0)
G2.loadFromFile(folderName, "condensedGraph.txt")
houseKeeper.compareGraphUnitTest(G, G2)
G.reportDummyUsefulNode()
G.reportEdge()
graphFileName = "condensedGraph.txt"
contigFile = "noEmbed_Double.fasta"
outContigFile = "improved.fasta"
outOpenList = "openZone.txt"
print "formSeqGraph: Outputting improved contigs from seqGraph to improved.fasta"
IORobot.readContigOut(folderName, mummerLink, graphFileName, contigFile,
outContigFile, outOpenList)
def observeOverlap(folderName):
dataList = alignerRobot.extractMumData(folderName, "selfOut")
dataList = alignerRobot.transformCoor(dataList)
lenDic = IORobot.obtainLength(folderName, 'contigs.fasta')
matchThres = 10000
nonMatchThres = 500
count = 0
newDataList = []
for eachitem in dataList:
name1, name2 = eachitem[-2], eachitem[-1]
matchLen1, matchLen2 = eachitem[4], eachitem[5]
start1, end1, start2, end2 = eachitem[0], eachitem[1], eachitem[
2], eachitem[3]
# if name1!= name2 and min(lenDic[name1] - end1, lenDic[name2] - end2 ) > nonMatchThres \
# and min(start1, start2) > nonMatchThres \
if name1!= name2 and ( min(lenDic[name1] - end1, lenDic[name2] - end2 ) > nonMatchThres \
or min(start1, start2) > nonMatchThres ) \
and matchLen1> matchThres:
print "eachitem ", eachitem, lenDic[name1], lenDic[name2]
count = count + 1
newDataList.append(eachitem)
print "Count: " + str(count)
blkDic = getBreakPointFromDataList(folderName, newDataList)
LCList = IORobot.loadContigsFromFile(folderName, "contigs.fasta")
contigList = []
for eachcontig in LCList:
#print eachcontig
if not eachcontig in blkDic:
contigList = contigList + [LCList[eachcontig]]
else:
contigList = contigList + tmpBreakAcBkPts(LCList[eachcontig],
blkDic[eachcontig])
print "len(contigList)", len(contigList)
IORobot.writeSegOut(contigList, folderName, "breakChains.fasta")
def runningTestSet(self ,myFolderName, ctexpected):
print "Integration test on FinisherSC: " + myFolderName
self.sourceFolder = myFolderName
os.system("mkdir " + self.testingFolder)
for eachitem in self.listOfFiles:
os.system("cp "+ self.sourceFolder + eachitem + " " +self.testingFolder)
os.system("python finisherSC.py -par 4 "+ self.testingFolder + " "+ self.mummerPath)
lenDic = IORobot.obtainLength(self.testingFolder, "/improved3.fasta")
print lenDic
assert(len(lenDic) == ctexpected)
os.system("rm -rf "+ self.testingFolder)
def runningTestSet(self ,myFolderName, ctexpected):
print "Integration test on FinisherSC: " + myFolderName
self.sourceFolder = myFolderName
os.system("mkdir " + self.testingFolder)
for eachitem in self.listOfFiles:
os.system("cp "+ self.sourceFolder + eachitem + " " +self.testingFolder)
os.system("python finisherSC.py -par 4 "+ self.testingFolder + " "+ self.mummerPath)
lenDic = IORobot.obtainLength(self.testingFolder, "/improved3.fasta")
print lenDic
assert(len(lenDic) == ctexpected)
os.system("rm -rf "+ self.testingFolder)
def getBreakPointFromDataList(folderName, dataList):
g = 1000
blkDic = {}
dataList.sort(key=itemgetter(-2))
lenDic = IORobot.obtainLength(folderName, "contigs.fasta")
json_data = open(folderName + "modifiedOutliners.json", 'r')
breakPtsDic = json.load(json_data)
sep = 5000
for key, items in groupby(dataList, itemgetter(-2)):
contigName = key
newList = []
for eachitem in items:
newList.append([eachitem[0], eachitem[1]])
newList.sort()
bktmp = [0]
if newList[0][0] > g:
if withinBound(sep, breakPtsDic[contigName], newList[0][0]):
bktmp.append(newList[0][0])
#bktmp.append(newList[0][0])
for i in range(len(newList) - 1):
if newList[i + 1][0] > newList[i][1] + g:
if withinBound(sep, breakPtsDic[contigName],
newList[i + 1][0]):
bktmp.append(newList[i + 1][0])
bktmp.append(lenDic[contigName])
blkDic[contigName] = bktmp
print "contigName: " + contigName
print "bktmp:", bktmp
print "breakPtsDic[contigName]", breakPtsDic[contigName]
return blkDic
def formRelatedReadsFile(folderName, mummerLink):
# Find associated read and extract into a file associatedReads.fasta
# Input: contigs.fasta, cleaned_Reads.fasta
# Output: relatedReads.fasta
# ## Extract heads of the contigs
print ">formRelatedReadsFile"
f = open(folderName + "improved.fasta", 'r')
f2 = open(folderName + "improvedTrunc.fasta", 'w')
temp = f.readline()
tempContig = ""
thres = 400
runningIndex = 0
endThres = 10
while len(temp) > 0:
if temp[-1] == '\n':
temp = temp[0:-1]
if temp[0] == '>':
if len(tempContig) > 0:
IORobot.writeToFile(f2, runningIndex, tempContig[0:thres])
runningIndex = runningIndex + 1
IORobot.writeToFile(f2, runningIndex, tempContig[-thres:])
runningIndex = runningIndex + 1
IORobot.writeToFile(f2, runningIndex, houseKeeper.reverseComplement(tempContig[0:thres]))
runningIndex = runningIndex + 1
IORobot.writeToFile(f2, runningIndex, houseKeeper.reverseComplement(tempContig[-thres:]))
runningIndex = runningIndex + 1
tempContig = ""
else:
tempContig = tempContig + temp
temp = f.readline()
IORobot.writeToFile(f2, runningIndex, tempContig[0:thres])
runningIndex = runningIndex + 1
IORobot.writeToFile(f2, runningIndex, tempContig[-thres:])
runningIndex = runningIndex + 1
IORobot.writeToFile(f2, runningIndex, houseKeeper.reverseComplement(tempContig[0:thres]))
runningIndex = runningIndex + 1
IORobot.writeToFile(f2, runningIndex, houseKeeper.reverseComplement(tempContig[-thres:]))
runningIndex = runningIndex + 1
f2.close()
f.close()
# ## Write double stranded reads
IORobot.writeToFile_Double1(folderName, "improved.fasta", "improved_Double.fasta", "contig")
# writeToFile_Double1(folderName, "raw_reads.fasta", "raw_reads_Double.fasta","read")
# ## Apply MUMMER on them using cleanedReads against them
assoiatedReadIndex = []
nameList = []
numberOfFiles = max(20, houseKeeper.globalParallel)
if True:
bindir = os.path.abspath(os.path.dirname(sys.argv[0]))
command = bindir + "/fasta-splitter.pl --n-parts " + str(numberOfFiles) + " " + folderName + houseKeeper.globalReadName
os.system(command)
workerList = []
for dummyI in range(1, numberOfFiles + 1):
indexOfMum = ""
if dummyI < 10:
indexOfMum = "0" + str(dummyI)
else:
indexOfMum = str(dummyI)
outputName, referenceName, queryName, specialName= "outGapFillRaw"+indexOfMum , "improvedTrunc.fasta", houseKeeper.globalReadName[0:-6] + ".part-" + indexOfMum + ".fasta", "fromMum" + indexOfMum
workerList.append([outputName, referenceName, queryName, specialName])
if True:
alignerRobot.useMummerAlignBatch(mummerLink, folderName, workerList, houseKeeper.globalParallel ,True)
# alignerRobot.useMummerAlign(mummerLink, folderName, "out", "improvedTrunc.fasta", "raw_reads.part-" + indexOfMum + ".fasta", True, "fromMum" + indexOfMum )
'''
command = mummerLink + "nucmer --maxmatch --nosimplify -p " + folderName + "out " + folderName + "improvedTrunc.fasta raw_reads.part-" + indexOfMum + ".fasta"
os.system(command)
command = mummerLink + "show-coords -r " + folderName + "out.delta > " + folderName + "fromMum" + indexOfMum
os.system(command)
'''
for dummyI in range(1, numberOfFiles + 1):
indexOfMum = ""
if dummyI < 10:
indexOfMum = "0" + str(dummyI)
else:
indexOfMum = str(dummyI)
f = open(folderName + "fromMum" + indexOfMum, 'r')
for i in range(6):
tmp = f.readline()
while len(tmp) > 0:
infoArr = tmp.split('|')
myArr = infoArr[-1].split('\t')
rdGpArr = infoArr[-1].split('\t')
contigName = rdGpArr[0].rstrip().lstrip()
readName = rdGpArr[1].rstrip().lstrip()
endSegArr = infoArr[0].split(" ")
pos = []
for eachitem in endSegArr:
if len(eachitem) > 0:
pos.append(int(eachitem))
startPos = pos[0]
endPos = pos[1]
if startPos < endThres and endPos > thres - endThres:
assoiatedReadIndex.append(myArr[1])
nameList.append([int(contigName.split('_')[1]), readName])
tmp = f.readline()
f.close()
nameList.sort()
assoiatedReadIndex.sort()
# print "assoiatedReadIndex", assoiatedReadIndex
ckIndex = 0
f = open(folderName + "associatedNames.txt", 'w')
oneItem = 0
keyFound = []
for key, items in groupby(assoiatedReadIndex):
countItem = 0
for eachitem in items:
countItem += 1
if countItem == 1:
oneItem += 1
else:
key = key.rstrip()
if not key in keyFound:
f.write(key + '\n')
keyFound.append(key)
ckIndex += 1
print "ckIndex,oneItem: ", ckIndex, oneItem
f.close()
fFilter = open(folderName + "associatedNames.txt", 'r')
fout = open(folderName + "associatedNames2.txt", 'w')
maxCount = 12000
mytmpDum = fFilter.readline()
i = 0
while i < maxCount and len(mytmpDum) > 0:
fout.write(mytmpDum)
mytmpDum = fFilter.readline()
i = i + 1
fout.close()
fFilter.close()
command = "perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' " + folderName + "associatedNames2.txt " + folderName + houseKeeper.globalReadName +" > " + folderName + "relatedReads.fasta"
os.system(command)
IORobot.writeToFile_Double1(folderName, "relatedReads.fasta", "relatedReads_Double.fasta", "read")
def writeContigReadCombine(blockedSet, dataSet, folderName, rawReadList, numberOfContig, contigList, leftConnect, option, rightConnect, mummerLink):
# ## repeat aware logging
# print "myExtraLinkList", myExtraLinkList
# ## end repeat aware logging
myExtraLinkList = loggingReadsToRepeat(blockedSet + dataSet, contigList)
i = 0
fOriginal = open(folderName + "improved.fasta", 'r')
readSet = []
tmp = fOriginal.readline().rstrip()
tmpRead = ""
while len(tmp) > 0:
if tmp[0] == '>':
if len(tmpRead) > 0:
readSet.append(tmpRead)
tmpRead = ""
else:
tmpRead = tmpRead + tmp
tmp = fOriginal.readline().rstrip()
readSet.append(tmpRead)
fOriginal.close()
# ## Put the needed rawReads into the RAM using Dictionary
fAppendRaw = open(folderName + "appendRaw.txt", 'w')
for eachraw in rawReadList:
fAppendRaw.write(eachraw)
fAppendRaw.write('\n')
fAppendRaw.close()
command = "perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' " + folderName + "appendRaw.txt " + folderName + "relatedReads_Double.fasta > " + folderName + "rawToAppend.fasta"
os.system(command)
rawRead = {}
fOriginal = open(folderName + "rawToAppend.fasta", 'r')
tmp = fOriginal.readline().rstrip()
tmpRead = ""
tmpName = ""
while len(tmp) > 0:
if tmp[0] == '>':
if len(tmpRead) > 0:
rawRead[tmpName] = tmpRead
tmpRead = ""
tmpName = tmp[1:]
else:
tmpRead = tmpRead + tmp
tmp = fOriginal.readline().rstrip()
rawRead[tmpName] = tmpRead
# ## End
seqToPrint = []
contigUsed = [False for i in range(numberOfContig / 2)]
storedStrand = [[-1, 'n'] for i in range(numberOfContig)]
finalList = []
for eachContig, i in zip(contigList, range(len(contigList))):
tmpList = []
for eachitem in eachContig:
readNum = eachitem / 2
if contigUsed[readNum] == False:
seqToPrint.append(eachitem)
tmpList.append(eachitem)
contigUsed[readNum] = True
# ## mark ouput strandinfo
storedStrand[eachitem] = [len(finalList), 'p']
if len(tmpList) > 0:
finalList.append(tmpList)
for kkk in range(len(storedStrand)):
if storedStrand[kkk][1] == 'n':
if kkk % 2 == 0:
storedStrand[kkk][0] = storedStrand[kkk + 1][0]
storedStrand[kkk][1] = 'd'
else:
storedStrand[kkk][0] = storedStrand[kkk - 1][0]
storedStrand[kkk][1] = 'd'
# ## begin stored output blocked pairs
blockExtraStored(storedStrand, myExtraLinkList, folderName)
# ## end output blocked pairs stored
fImproved = open(folderName + "improved2.fasta", 'w')
for eachcontig, dummyIndex in zip(finalList, range(len(finalList))):
fImproved.write(">Segkk" + str(dummyIndex) + '\n')
tmpStore = -1997
tmpStore2 = -1998
tmpStore3 = -1999
for eachseg, hidum in zip(eachcontig, range(len(eachcontig))):
readNum = eachseg / 2
orientation = eachseg % 2
newStart = 0
# Begin hack
### old statement
x , y , l = tmpStore, leftConnect[eachseg][1], tmpStore2
### End old statement
if hidum == 0:
x , y , l = tmpStore, leftConnect[eachseg][1], tmpStore2
else:
prevseg = eachcontig[hidum-1]
prevReadNum = prevseg/2
prevOrient = prevseg %2
if prevOrient == 0:
leftSeg = readSet[prevReadNum]
else:
leftSeg = houseKeeper.reverseComplement(readSet[prevReadNum])
rightSeg = tmpStore3
overlapX = IORobot.align(leftSeg, rightSeg, folderName, mummerLink)
leftSeg = tmpStore3
if orientation == 0:
rightSeg = readSet[readNum]
else:
rightSeg = houseKeeper.reverseComplement(readSet[readNum])
overlapY = IORobot.align(leftSeg, rightSeg, folderName, mummerLink)
print "Before : x, y , l : ", x, y , l
x = overlapX[1]
y = overlapY[0]
l = tmpStore2
print "After : x, y , l : ", x, y , l
# End hack
extraRead = ""
if hidum == 0:
newStart = 0
else:
if l < x + y:
# begin hack
### old statement
newStart = x + y - l
### end old statement
prevseg = eachcontig[hidum-1]
prevReadNum = prevseg/2
prevOrient = prevseg %2
if prevOrient == 0:
leftSeg = readSet[prevReadNum]
else:
leftSeg = houseKeeper.reverseComplement(readSet[prevReadNum])
if orientation == 0:
rightSeg = readSet[readNum]
else:
rightSeg = houseKeeper.reverseComplement(readSet[readNum])
print "Before : ", newStart
overlapNewStart = IORobot.align(leftSeg, rightSeg, folderName, mummerLink)
newStart = overlapNewStart[1]
print "After : ", newStart
# end hack
else:
newStart = 0
if option == 'polish':
print "Missing polish"
extraRead = tmpStore3[x:l - y]
# extraRead = performPolishing(leftConnect[eachseg][0], eachseg, tmpStore3[x:l-y], dataSet, folderName)
else:
extraRead = tmpStore3[x:l - y]
print extraRead[0:10], len(extraRead)
fImproved.write(extraRead)
if orientation == 0:
fImproved.write(readSet[readNum][newStart:])
else:
fImproved.write(houseKeeper.reverseComplement(readSet[readNum])[newStart:])
if rightConnect[eachseg][1] != -1:
tmpStore = rightConnect[eachseg][1]
tmpStore2 = len(rawRead[rightConnect[eachseg][2]])
tmpStore3 = rawRead[rightConnect[eachseg][2]]
fImproved.write('\n')
fImproved.close()
def extractEdgeSet(folderName, mummerLink, option="nopolish"):
# Tasks: reconstruct the string graph
# Input : relatedReads_Double.fasta, conig_Double.fasta
# Intermediate files: fromMum_overlap , fromMum_overlap
# Output: connectivity of eachNode: InList, OutList [critical]
# connectivity of eachNode: arrow representation with size [optional]
# ## Perform MUMMER alignment
print ">Extract Edge set"
contigOnlyLengthDic = IORobot.obtainLength(folderName, "improved.fasta")
# print lengthDic
lengthDic = IORobot.findContigLength(folderName, "improved")
numberOfContig = len(contigOnlyLengthDic)*2
K = 400
thres = 5
# ## Apply MUMMER on them using cleanedReads against them
IORobot.truncateEndOfContigs(folderName, "improved_Double.fasta", "smaller_improvedContig.fasta", 25000, lengthDic)
dataSet = []
numberOfFiles = max(20, houseKeeper.globalParallel)
if True:
bindir = os.path.abspath(os.path.dirname(sys.argv[0]))
command = bindir + "/fasta-splitter.pl --n-parts " + str(numberOfFiles) + " " + folderName + "relatedReads_Double.fasta"
os.system(command)
workerList = []
for dummyI in range(1, numberOfFiles + 1):
indexOfMum = ""
if dummyI < 10:
indexOfMum = "0" + str(dummyI)
else:
indexOfMum = str(dummyI)
outputName, referenceName, queryName, specialName= "outGapFillRefine"+indexOfMum , "smaller_improvedContig.fasta", "relatedReads_Double.part-" + indexOfMum + ".fasta", "fromMumRefine" + indexOfMum
workerList.append([outputName, referenceName, queryName, specialName])
if True:
alignerRobot.useMummerAlignBatch(mummerLink, folderName, workerList, houseKeeper.globalParallel ,True)
# alignerRobot.useMummerAlign(mummerLink, folderName, "outRefine", "smaller_improvedContig.fasta", "relatedReads_Double.part-" + indexOfMum + ".fasta", True, "fromMumRefine" + indexOfMum)
for dummyI in range(1, numberOfFiles + 1):
tmpSet = IORobot.obtainLinkInfoReadContig(dummyI, mummerLink, folderName,thres, lengthDic, K)
dataSet = dataSet + tmpSet
# ## repeat aware
usableJunction = loadOpenList(folderName)
dataSet, blockedSet = filterRepeatEnd(dataSet, usableJunction)
# ## repeat aware end
dataSet.sort()
matchPair = formMatchPairFromReadInfo(dataSet)
# Bug fix on repeat detection from reads alone
matchPair = filterRepeatPair(matchPair)
# end bug fix
# print matchPair
bestMatchPair = []
for key, items in groupby(matchPair, itemgetter(0, 1)):
maxvalue = -1
maxLenPair = []
for eachitem in items:
if eachitem[2] > maxvalue:
maxvalue = eachitem[2]
maxLenPair = [eachitem[3], eachitem[4], eachitem[5]]
bestMatchPair.append([key[0], key[1], maxvalue, maxLenPair[0], maxLenPair[1], maxLenPair[2]])
contigList, leftConnect, rightConnect, rawReadList = formbestpair(bestMatchPair,numberOfContig)
print "contigList", contigList
writeContigReadCombine(blockedSet, dataSet, folderName, rawReadList, numberOfContig, contigList, leftConnect, option, rightConnect, mummerLink)
def xPhased(folderName , mummerLink):
# ## Repeat resolution [Proxy for MB]
# 1. Re-form the contig string graph with ALL connections from contigs only V
# 2. Log down the reads and associated blocked contigs V
# 3. Use reads to connect;
# 4. Transform graph by identifying 1 successor/predecessor case ; Condense(important);
# 5. Read out contigs
numberOfContig, dataSet = IORobot.obtainLinkInfo(folderName, mummerLink, "improved2", "mb")
lenDic = IORobot.obtainLength(folderName, "improved2_Double.fasta")
confidenLenThres = 0
G = graphLib.seqGraph(numberOfContig)
extraEdges = loadEdgeFromBlockedReads(folderName)
for eachitem in dataSet:
# print eachitem
wt, myin, myout = eachitem
myInData = myin[6:].split('_')
myOutData = myout[6:].split('_')
if myInData[1] == 'p':
offsetin = 0
else:
offsetin = 1
if myOutData[1] == 'p':
offsetout = 0
else:
offsetout = 1
i = int(myInData[0]) * 2 + offsetin
j = int(myOutData[0]) * 2 + offsetout
ck = False
for eachedge in extraEdges:
mystart, myend, len1, len2 = eachedge[0], eachedge[1], eachedge[2] , eachedge[3]
if [i, j] == [mystart, myend] and min(len1, len2) >= wt and lenDic[myin] >= confidenLenThres and lenDic[myout] >= confidenLenThres:
ck = True
if ck:
G.insertEdge(i, j, wt)
# G.reportEdge()
G.MBResolve()
G.reportEdge()
G.saveToFile(folderName, "condensedGraphMB.txt")
graphFileName = "condensedGraphMB.txt"
contigFile = "improved2_Double.fasta"
outContigFile = "improved3.fasta"
outOpenList = "openZoneMB.txt"
IORobot.readContigOut(folderName, mummerLink, graphFileName, contigFile, outContigFile, outOpenList)
# ## Repeat resolution [Proxy for phasing step]
# 6. Find out the repeat region by MSA
# 7. Find out the location of SNPs and extend across repeat
# [short cut : use contig creator : your job here is to get data into the correct formats]
print "xPhased"
def fetchSuccessor(folderName , mummerLink):
print "fetchSuccessor"
left_connect, right_connect = [], []
print "Direct greedy"
print "fetchSuccessor: Aligning non-contained contigs to themselves, output files are greedy*.delta"
numberOfContig, dataSet = IORobot.obtainLinkInfo(folderName, mummerLink, "noEmbed", "greedy")
# [next_item, overlap_length]
leftConnect = [[-1, -1] for i in range(numberOfContig)]
rightConnect = [[-1, -1] for i in range(numberOfContig)]
dataSet.sort(reverse=True, key=itemgetter(1))
print "fetchSuccessor: Finding best successors"
for key, items in groupby(dataSet, itemgetter(1)):
# if key == "Contig217_d":
# print "dddd"
maxVal = -1
myName = key
connectorName = ""
for eachsubitem in items:
if eachsubitem[0] > maxVal:
maxVal = eachsubitem[0]
connectorName = eachsubitem[2]
prefix = myName.split('_')
suffix = connectorName.split('_')
lengthOfOverlap = maxVal
if prefix[1] == 'p':
prefixContig = int(prefix[0][6:]) * 2
else:
prefixContig = int(prefix[0][6:]) * 2 + 1
if suffix[1] == 'p':
suffixContig = int(suffix[0][6:]) * 2
else:
suffixContig = int(suffix[0][6:]) * 2 + 1
assert(rightConnect[prefixContig][0] == -1)
rightConnect[prefixContig][0] = suffixContig
rightConnect[prefixContig][1] = lengthOfOverlap
dataSet.sort(reverse=True, key=itemgetter(2))
print "fetchSuccessor: Finding best predecessors"
for key, items in groupby(dataSet, itemgetter(2)):
maxVal = -1
myName = key
connectorName = ""
for eachsubitem in items:
if eachsubitem[0] > maxVal:
maxVal = eachsubitem[0]
connectorName = eachsubitem[1]
prefix = connectorName.split('_')
suffix = myName.split('_')
lengthOfOverlap = maxVal
if prefix[1] == 'p':
prefixContig = int(prefix[0][6:]) * 2
else:
prefixContig = int(prefix[0][6:]) * 2 + 1
if suffix[1] == 'p':
suffixContig = int(suffix[0][6:]) * 2
else:
suffixContig = int(suffix[0][6:]) * 2 + 1
assert(leftConnect[suffixContig][0] == -1)
leftConnect[suffixContig][0] = prefixContig
leftConnect[suffixContig][1] = lengthOfOverlap
print "fetchSuccessor: Outputting best successors to rightConnect.txt"
# ## Write to file:
f = open(folderName + 'rightConnect.txt', 'w')
for eachitem, dummyIndex in zip(rightConnect, range(len(rightConnect))):
f.write(str(dummyIndex) + ',' + str(eachitem[0]) + ',' + str(eachitem[1]) + '\n')
f.close()
print "fetchSuccessor: Outputting best predecessors to leftConnect.txt"
f = open(folderName + 'leftConnect.txt', 'w')
for eachitem, dummyIndex in zip(leftConnect, range(len(leftConnect))):
f.write(str(dummyIndex) + ',' + str(eachitem[0]) + ',' + str(eachitem[1]) + '\n')
f.close()
def xPhased(folderName , mummerLink):
# ## Repeat resolution [Proxy for MB]
# 1. Re-form the contig string graph with ALL connections from contigs only V
# 2. Log down the reads and associated blocked contigs V
# 3. Use reads to connect;
# 4. Transform graph by identifying 1 successor/predecessor case ; Condense(important);
# 5. Read out contigs
print "xPhased: Aligning improved2.fasta against itself, outputting to mb*.delta"
numberOfContig, dataSet = IORobot.obtainLinkInfo(folderName, mummerLink, "improved2", "mb")
lenDic = IORobot.obtainLength(folderName, "improved2_Double.fasta")
confidenLenThres = 0
print "xPhased: Building seqGraph"
G = graphLib.seqGraph(numberOfContig)
extraEdges = loadEdgeFromBlockedReads(folderName)
for eachitem in dataSet:
# print eachitem
wt, myin, myout = eachitem
myInData = myin[6:].split('_')
myOutData = myout[6:].split('_')
if myInData[1] == 'p':
offsetin = 0
else:
offsetin = 1
if myOutData[1] == 'p':
offsetout = 0
else:
offsetout = 1
i = int(myInData[0]) * 2 + offsetin
j = int(myOutData[0]) * 2 + offsetout
ck = False
for eachedge in extraEdges:
mystart, myend, len1, len2 = eachedge[0], eachedge[1], eachedge[2] , eachedge[3]
if [i, j] == [mystart, myend] and min(len1, len2) >= wt and lenDic[myin] >= confidenLenThres and lenDic[myout] >= confidenLenThres:
ck = True
if ck:
G.insertEdge(i, j, wt)
# G.reportEdge()
G.MBResolve()
G.reportEdge()
print "xPhased: Saving condensed seqGraph to condensedGraphMB.txt"
G.saveToFile(folderName, "condensedGraphMB.txt")
graphFileName = "condensedGraphMB.txt"
contigFile = "improved2_Double.fasta"
outContigFile = "improved3.fasta"
outOpenList = "openZoneMB.txt"
print "xPhased: Outputting improved contigs from condensed seqGraph to improved3.fasta"
IORobot.readContigOut(folderName, mummerLink, graphFileName, contigFile, outContigFile, outOpenList)
# ## Repeat resolution [Proxy for phasing step]
# 6. Find out the repeat region by MSA
# 7. Find out the location of SNPs and extend across repeat
# [short cut : use contig creator : your job here is to get data into the correct formats]
print "xPhased"
def fetchSuccessor(folderName , mummerLink):
print "fetchSuccessor"
left_connect, right_connect = [], []
print "Direct greedy"
numberOfContig, dataSet = IORobot.obtainLinkInfo(folderName, mummerLink, "noEmbed", "greedy")
# [next_item, overlap_length]
leftConnect = [[-1, -1] for i in range(numberOfContig)]
rightConnect = [[-1, -1] for i in range(numberOfContig)]
dataSet.sort(reverse=True, key=itemgetter(1))
for key, items in groupby(dataSet, itemgetter(1)):
# if key == "Contig217_d":
# print "dddd"
maxVal = -1
myName = key
connectorName = ""
for eachsubitem in items:
if eachsubitem[0] > maxVal:
maxVal = eachsubitem[0]
connectorName = eachsubitem[2]
prefix = myName.split('_')
suffix = connectorName.split('_')
lengthOfOverlap = maxVal
if prefix[1] == 'p':
prefixContig = int(prefix[0][6:]) * 2
else:
prefixContig = int(prefix[0][6:]) * 2 + 1
if suffix[1] == 'p':
suffixContig = int(suffix[0][6:]) * 2
else:
suffixContig = int(suffix[0][6:]) * 2 + 1
assert(rightConnect[prefixContig][0] == -1)
rightConnect[prefixContig][0] = suffixContig
rightConnect[prefixContig][1] = lengthOfOverlap
dataSet.sort(reverse=True, key=itemgetter(2))
for key, items in groupby(dataSet, itemgetter(2)):
maxVal = -1
myName = key
connectorName = ""
for eachsubitem in items:
if eachsubitem[0] > maxVal:
maxVal = eachsubitem[0]
connectorName = eachsubitem[1]
prefix = connectorName.split('_')
suffix = myName.split('_')
lengthOfOverlap = maxVal
if prefix[1] == 'p':
prefixContig = int(prefix[0][6:]) * 2
else:
prefixContig = int(prefix[0][6:]) * 2 + 1
if suffix[1] == 'p':
suffixContig = int(suffix[0][6:]) * 2
else:
suffixContig = int(suffix[0][6:]) * 2 + 1
assert(leftConnect[suffixContig][0] == -1)
leftConnect[suffixContig][0] = prefixContig
leftConnect[suffixContig][1] = lengthOfOverlap
# ## Write to file:
f = open(folderName + 'rightConnect.txt', 'w')
for eachitem, dummyIndex in zip(rightConnect, range(len(rightConnect))):
f.write(str(dummyIndex) + ',' + str(eachitem[0]) + ',' + str(eachitem[1]) + '\n')
f.close()
f = open(folderName + 'leftConnect.txt', 'w')
for eachitem, dummyIndex in zip(leftConnect, range(len(leftConnect))):
f.write(str(dummyIndex) + ',' + str(eachitem[0]) + ',' + str(eachitem[1]) + '\n')
f.close()
