def coloringNodes():
folderName = "Apr10Test/"
if False:
alignerRobot.useMummerAlign("/usr/bin/", folderName, "debug", "reference.fasta", "LC_n.fasta")
dataList = alignerRobot.extractMumData(folderName, "debugOut")
dataList.sort(key = itemgetter(-1))
mappedDic = {}
for key, items in groupby(dataList, itemgetter(-1)):
print "key", key
matchLen = -1
for eachitem in items:
if eachitem[-4] > matchLen:
mappedDic[key] = eachitem[-2]
matchLen = eachitem[-4]
for eachitem in mappedDic:
if mappedDic[eachitem] == 'c3':
print str(int(eachitem[5:])*2)+"{color:blue}"
print str(int(eachitem[5:])*2+1)+"{color:blue}"
if mappedDic[eachitem] == 'c1':
print str(int(eachitem[5:])*2)+"{color:green}"
print str(int(eachitem[5:])*2+1)+"{color:green}"
def formExtraEdges(
folderName="/home/kakitfive/kkdata2/MetaFinisherSC/dataFolderBackup/",
optTypeFileHeader="phaseString",
contigFilename="improved3",
G=[],
N1=0):
dataList = alignerRobot.extractMumData(folderName,
optTypeFileHeader + "CR" + "Out")
dataList.sort(key=itemgetter(-2))
lenDic = IORobot.obtainLength(folderName, contigFilename + "_Double.fasta")
count = 0
tmpItem = []
embedContig2ReadDic, read2EmbedContigDic = {}, {}
for key, items in groupby(dataList, itemgetter(-2)):
isEmbedded = False
for eachitem in items:
#print eachitem
if eachitem[4] > lenDic[key] - 300:
isEmbedded = True
tmpItem = eachitem
if isEmbedded:
count = count + 1
readName = tmpItem[-1]
embedContig2ReadDic[key] = readName
read2EmbedContigDic[readName] = key
print "len(embedContig2ReadDic)", len(embedContig2ReadDic)
#assert(False)
for contigName in embedContig2ReadDic:
readName = embedContig2ReadDic[contigName]
readIndex, contigIndex = abunHouseKeeper.parseEdgeNameToID(
readName, 'R'), abunHouseKeeper.parseEdgeNameToID(contigName, 'C')
for eachprev in G.graphNodesList[readIndex].listOfPrevNodes:
idNode, wt = eachprev[0], eachprev[1]
if idNode < N1:
G.insertEdge(idNode, contigIndex, wt)
for eachnext in G.graphNodesList[readIndex].listOfNextNodes:
idNode, wt = eachnext[0], eachnext[1]
if idNode < N1:
G.insertEdge(contigIndex, idNode, wt)
return G
def decideCut(folderName, mummerPath):
'''
Input : directPath.fasta, indirectPath.fasta
Output : toDelete
'''
thres = 50
if True:
alignerRobot.useMummerAlign(mummerPath, folderName, \
"indirectvsdirect", "indirectPath.fasta", "directPath.fasta", specialForRaw = False, specialName = "", refinedVersion= True)
dataList = alignerRobot.extractMumData(folderName , "indirectvsdirectOut")
lenDic = IORobot.obtainLength(folderName, "directPath.fasta")
ctr =0
ctrindirect = 0
dataList.sort(key = itemgetter(-1))
toDelete = True
for key, items in groupby(dataList, itemgetter(-1)):
print "key", key
ctr = ctr + 1
isFound = False
for eachitem in items:
if eachitem[2] < thres and eachitem[3] > lenDic[key] - thres:
isFound = True
if isFound:
ctrindirect = ctrindirect + 1
epsilon = 1.1
print "ctrindirect, ctr", ctrindirect, ctr
if ctrindirect*1.0/ctr < (1- epsilon):
toDelete = False
else:
toDelete = True
return toDelete
def decideCut(folderName, mummerPath):
'''
Input : directPath.fasta, indirectPath.fasta
Output : toDelete
'''
thres = 50
if True:
alignerRobot.useMummerAlign(mummerPath, folderName, \
"indirectvsdirect", "indirectPath.fasta", "directPath.fasta", specialForRaw = False, specialName = "", refinedVersion= True)
dataList = alignerRobot.extractMumData(folderName , "indirectvsdirectOut")
lenDic = IORobot.obtainLength(folderName, "directPath.fasta")
ctr =0
ctrindirect = 0
dataList.sort(key = itemgetter(-1))
toDelete = True
for key, items in groupby(dataList, itemgetter(-1)):
print "key", key
ctr = ctr + 1
isFound = False
for eachitem in items:
if eachitem[2] < thres and eachitem[3] > lenDic[key] - thres:
isFound = True
if isFound:
ctrindirect = ctrindirect + 1
epsilon = 1.1
print "ctrindirect, ctr", ctrindirect, ctr
if ctrindirect*1.0/ctr < (1- epsilon):
toDelete = False
else:
toDelete = True
return toDelete
def mapStrangePairs():
folderName = "Apr10Test/"
json_data = open(folderName + "furtherGapList.json", 'r')
furtherGapList = json.load(json_data)
segLookUp = IORobot.readContigsFromFile(folderName, "LC_n_Double.fasta")
f = open(folderName + "wrongCondense.fasta", 'w')
ctr = 0
for eachitem in furtherGapList:
beforeI, afterI = eachitem[0], eachitem[1]
f.write(">Segkk"+str(ctr)+"\n")
f.write(segLookUp[beforeI]+"\n")
ctr = ctr + 1
f.write(">Segkk"+str(ctr)+"\n")
f.write(segLookUp[afterI]+"\n")
ctr = ctr + 1
f.close()
if False:
alignerRobot.useMummerAlign("/usr/bin/", folderName, "wrongCondenseDebug", "reference.fasta", "wrongCondense.fasta")
dataList = alignerRobot.extractMumData(folderName, "wrongCondenseDebugOut")
dataList.sort(key = itemgetter(-1))
mappedDic = {}
for key, items in groupby(dataList, itemgetter(-1)):
print "key", key
matchLen = -1
for eachitem in items:
if eachitem[-4] > matchLen:
mappedDic[key] = eachitem
matchLen = eachitem[-4]
for eachitem in mappedDic:
print "results : ", eachitem, mappedDic[eachitem]
def formSortedDataList(folderName):
sortedContigList, sortedReadList, sortedContigDic, sortedReadDic =\
[], [] , {}, {}
dataList = alignerRobot.extractMumData(folderName, "phaseStringCROut")
sortedContigList = sorted(dataList, key=itemgetter(-2))
sortedContigDic[sortedContigList[0][-2]] = 0
for i in range(1, len(sortedContigList)):
if sortedContigList[i][-2] != sortedContigList[i - 1][-2]:
sortedContigDic[sortedContigList[i][-2]] = i
sortedReadList = sorted(dataList, key=itemgetter(-1))
sortedReadDic[sortedReadList[0][-1]] = 0
for i in range(1, len(sortedReadList)):
if sortedReadList[i][-1] != sortedReadList[i - 1][-1]:
sortedReadDic[sortedReadList[i][-1]] = i
return sortedContigList, sortedReadList, sortedContigDic, sortedReadDic
def formSortedDataList(folderName):
sortedContigList, sortedReadList, sortedContigDic, sortedReadDic =\
[], [] , {}, {}
dataList = alignerRobot.extractMumData(folderName, "phaseStringCROut")
sortedContigList = sorted(dataList, key = itemgetter(-2))
sortedContigDic[sortedContigList[0][-2]] = 0
for i in range(1, len(sortedContigList)):
if sortedContigList[i][-2] != sortedContigList[i-1][-2]:
sortedContigDic[sortedContigList[i][-2]] = i
sortedReadList = sorted(dataList, key = itemgetter(-1))
sortedReadDic[sortedReadList[0][-1]] = 0
for i in range(1, len(sortedReadList)):
if sortedReadList[i][-1] != sortedReadList[i-1][-1]:
sortedReadDic[sortedReadList[i][-1]] = i
return sortedContigList, sortedReadList, sortedContigDic, sortedReadDic
def generateAbundanceGraph(folderName, mummerLink):
print "generateAbundanceGraph"
"""
1. Find your favorite mappers to map read back
a. MUMmer, Bowtie, bbmap, any that works V
b. And then write a short parser to parse the results V
"""
numberOfFiles = 20
workerList = []
for dummyI in range(1, numberOfFiles + 1):
indexOfMum = ""
if dummyI < 10:
indexOfMum = "0" + str(dummyI)
else:
indexOfMum = str(dummyI)
"""
"outGapFillRefine"+indexOfMum , "smaller_improvedContig.fasta", "relatedReads_Double.part-" + indexOfMum + ".fasta", "fromMumRefine" + indexOfMum
"""
outputName, referenceName, queryName, specialName = (
"outAbun" + indexOfMum,
"improved3.fasta",
"raw_reads.part-" + indexOfMum + ".fasta",
"outAbun" + indexOfMum,
)
workerList.append([outputName, referenceName, queryName, specialName])
if True:
alignerRobot.useMummerAlignBatch(mummerLink, folderName, workerList, houseKeeper.globalParallel, False)
"""
command = mummerLink + "nucmer --maxmatch --nosimplify -p " + folderName + "out " + folderName + "improved3.fasta "+folderName+"raw_reads.part-" + indexOfMum + ".fasta"
os.system(command)
command = mummerLink + "show-coords -r " + folderName + "out.delta > " + folderName + "fromMumAbun" + indexOfMum
os.system(command)
"""
dataList = []
for i in range(1, 1 + numberOfFiles):
if i < 10:
indexOfMum = "0" + str(i)
else:
indexOfMum = str(i)
dataList = dataList + alignerRobot.extractMumData(folderName, "outAbun" + str(indexOfMum) + "Out")
"""
2. Calculate count on the abundances
a. Aggregate by taking average [put weights on bin along contigs]
b. Inheritance and a subclass
"""
lenDic = IORobot.obtainLength(folderName, "improved3.fasta")
readLenDic = IORobot.obtainLength(folderName, "raw_reads.fasta")
myCountDic = {}
for eachitem in lenDic:
myCountDic[eachitem] = [0 for i in range(lenDic[eachitem])]
thres = 30
lenSum = 0
extraDataList = []
print "len(dataList)", len(dataList)
if not abunHouseKeeper.abunGlobalAvoidrefine:
myCountDic = evaluateCoverage(dataList, lenDic, readLenDic, folderName, mummerLink, True)
extraDataList = alignerRobot.extractMumData(folderName, "abunMissOut")
else:
extraDataList = []
dataList = dataList + extraDataList
myCountDic = evaluateCoverage(dataList, lenDic, readLenDic, folderName, mummerLink, False)
with open(folderName + "myCountDic.json", "w") as f:
json.dump(myCountDic, f)
return myCountDic
def getAllAssociatedReads(folderName, mummerLink,forFastaName):
'''
Input : relatedReads.fasta, raw_reads.fasta
Output : all_associated_reads.fasta
Algorithm :
a) Get all the associated reads
b) Loop for N=1 times : ==> this correspond 4 reads to link between the bridge in total
i) Align the raws and tmp_seedReads
ii) Put the new reads into the SeedReads
'''
header, referenceFile, queryFile = "seedReads", forFastaName + ".fasta" , "raw_reads.fasta"
gapFiller.formRelatedReadsFile(folderName, mummerLink, "improved3")
command = "cp " + folderName + "relatedReads.fasta " + folderName + referenceFile
os.system(command)
N = abunHouseKeeper.abunGlobalReadSearchDepth
print "N: ", N
if N >0 :
for trial in range(N):
print "trial", trial
numberOfFiles = houseKeeper.globalParallelFileNum
if True:
workerList = []
for dummyI in range(1, numberOfFiles + 1):
indexOfMum = ""
if dummyI < 10:
indexOfMum = "0" + str(dummyI)
else:
indexOfMum = str(dummyI)
outputName, referenceName, queryName, specialName= header+indexOfMum, referenceFile, "raw_reads.part-"+ indexOfMum + ".fasta", header + indexOfMum
workerList.append([outputName, referenceName, queryName, specialName])
alignerRobot.useMummerAlignBatch(mummerLink, folderName, workerList, houseKeeper.globalParallel ,False)
dataList = []
for i in range(1, 1+numberOfFiles):
if i < 10:
indexOfMum = "0" + str(i)
else:
indexOfMum = str(i)
dataList = dataList+ alignerRobot.extractMumData(folderName, header+ str(indexOfMum)+"Out")
filterList = []
lenDicRR = IORobot.obtainLength(folderName, queryFile)
print "len(dataList)", len(dataList)
for eachitem in dataList:
if checkSatisfy(eachitem, lenDicRR):
filterList.append(eachitem)
filterList.sort(key=itemgetter(-1))
newReads = []
for key, items in groupby(filterList, itemgetter(-1)):
newReads.append(key)
f = open(folderName + forFastaName + ".txt", 'w')
for eachitem in newReads:
f.write(eachitem + "\n")
f.close()
command = "perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' " + folderName + forFastaName + ".txt " + folderName + "raw_reads.fasta > " + folderName + forFastaName + ".fasta"
os.system(command)
else:
os.system("cp " + folderName + "relatedReads.fasta " + folderName + forFastaName + ".fasta")
def formReadContigStringGraph(folderName,
mummerLink,
contigFilename,
readsetFilename,
optTypeFileHeader,
graphName,
needAlignment=True):
'''
Input : all_associated_reads.fasta, improved3.fasta
Output : (G) String Graph linking the reads and contigs
Algorithm:
a) Form double reads and contigs V
b) Mummer the data and extract dataList three times V
c) Use the subroutine to output a graph V
d) Output the graph to a file phasing_String_graph.graph V
'''
G = []
IORobot.writeToFile_Double1(folderName, contigFilename + ".fasta",
contigFilename + "_Double.fasta", "contig")
IORobot.writeToFile_Double1(folderName, readsetFilename + ".fasta",
readsetFilename + "_Double.fasta", "reads")
header, referenceFile, queryFile = optTypeFileHeader + "CC", contigFilename + "_Double.fasta", contigFilename + "_Double.fasta"
#if needAlignment:
# alignerRobot.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile)
if needAlignment:
alignerRobot.useMummerAlignBatch(
mummerLink, folderName, [[header, referenceFile, queryFile, ""]],
houseKeeper.globalParallel)
lenDicCC = IORobot.obtainLength(folderName,
contigFilename + "_Double.fasta")
dataListCC = alignerRobot.extractMumData(folderName, header + "Out")
dataListCC = abunHouseKeeper.filterData(dataListCC, lenDicCC)
header, referenceFile, queryFile = optTypeFileHeader + "RR", readsetFilename + "_Double.fasta", readsetFilename + "_Double.fasta"
lenDicRR = IORobot.obtainLength(folderName,
readsetFilename + "_Double.fasta")
if not abunHouseKeeper.abunGlobalRRDisable:
if needAlignment:
alignerSubRoutine(folderName, referenceFile, queryFile, mummerLink,
header)
dataListRR = alignerRobot.extractMumData(folderName, header + "Out")
dataListRR = abunHouseKeeper.filterData(dataListRR, lenDicRR)
dataListRR = abunHouseKeeper.filterDataIdentical(dataListRR, lenDicRR)
else:
dataListRR = []
header, referenceFile, queryFile = optTypeFileHeader + "CR", contigFilename + "_Double.fasta", readsetFilename + "_Double.fasta"
if needAlignment:
alignerSubRoutine(folderName, referenceFile, queryFile, mummerLink,
header)
lenDicCR = dict(lenDicCC.items() + lenDicRR.items())
dataListCR = alignerRobot.extractMumData(folderName, header + "Out")
dataListCR = abunHouseKeeper.filterData(dataListCR, lenDicCR)
numberOfNodes = len(lenDicCR)
G = graphLib.seqGraph(numberOfNodes)
N1, N2 = len(lenDicCC), len(lenDicRR)
print "N1, N2, numberOfNodes: ", N1, N2, numberOfNodes
'''
e.g. of dataListCC[0], dataListRR[0], dataListCR[0]
[1, 520, 2913194, 2913716, 520, 523, 99.05, 'Contig0_d', 'Contig2_d']
[1, 1383, 1253, 2603, 1383, 1351, 82.39, 'Read0_d', 'Read1705_p']
[1, 718, 4334, 5074, 718, 741, 91.91, 'Contig0_d', 'Read1018_d']
'''
addDataToList(dataListCC, G, 0, 0, 'C', 'C')
addDataToList(dataListRR, G, N1, N1, 'R', 'R')
addDataToList(dataListCR, G, 0, N1, 'C', 'R')
Gnew = formExtraEdges(folderName, optTypeFileHeader, contigFilename, G, N1)
Gnew.saveToFile(folderName, graphName)
print "len(Gnew.graphNodesList)", len(Gnew.graphNodesList)
def formReadContigStringGraph(folderName, mummerLink, contigFilename, readsetFilename, optTypeFileHeader, graphName):
'''
Input : all_associated_reads.fasta, improved3.fasta
Output : (G) String Graph linking the reads and contigs
Algorithm:
a) Form double reads and contigs V
b) Mummer the data and extract dataList three times V
c) Use the subroutine to output a graph V
d) Output the graph to a file phasing_String_graph.graph V
'''
G = []
IORobot.writeToFile_Double1(folderName, contigFilename + ".fasta", contigFilename + "_Double.fasta", "contig")
IORobot.writeToFile_Double1(folderName, readsetFilename + ".fasta", readsetFilename + "_Double.fasta", "reads")
header, referenceFile, queryFile = optTypeFileHeader + "CC", contigFilename + "_Double.fasta" , contigFilename + "_Double.fasta"
if True:
alignerRobot.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile)
lenDicCC = IORobot.obtainLength(folderName, contigFilename + "_Double.fasta")
dataListCC = alignerRobot.extractMumData(folderName, header + "Out")
dataListCC = abunHouseKeeper.filterData(dataListCC, lenDicCC)
header, referenceFile, queryFile = optTypeFileHeader + "RR", readsetFilename + "_Double.fasta" , readsetFilename + "_Double.fasta"
lenDicRR = IORobot.obtainLength(folderName, readsetFilename + "_Double.fasta")
if not abunHouseKeeper.abunGlobalRRDisable:
if True:
alignerSubRoutine(folderName ,referenceFile, queryFile, mummerLink, header )
dataListRR = alignerRobot.extractMumData(folderName, header + "Out")
dataListRR = abunHouseKeeper.filterData(dataListRR, lenDicRR)
for eachitem in dataListRR:
if eachitem[-2] == "Read164_p" and eachitem[-1] == "Read159_p" :
print "debug" , eachitem
if eachitem[-1] == "Read164_p" and eachitem[-2] == "Read159_p" :
print "debug" , eachitem
dataListRR = abunHouseKeeper.filterDataIdentical(dataListRR, lenDicRR)
else:
dataListRR = []
header, referenceFile, queryFile = optTypeFileHeader + "CR", contigFilename + "_Double.fasta" , readsetFilename + "_Double.fasta"
if True:
alignerSubRoutine(folderName ,referenceFile, queryFile, mummerLink, header )
#alignerRobot.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile)
lenDicCR = dict(lenDicCC.items() + lenDicRR.items())
dataListCR = alignerRobot.extractMumData(folderName, header + "Out")
dataListCR = abunHouseKeeper.filterData(dataListCR, lenDicCR)
numberOfNodes = len(lenDicCR)
G = graphLib.seqGraph(numberOfNodes)
N1, N2 = len(lenDicCC), len(lenDicRR)
print "N1, N2, numberOfNodes: ", N1, N2, numberOfNodes
'''
e.g. of dataListCC[0], dataListRR[0], dataListCR[0]
[1, 520, 2913194, 2913716, 520, 523, 99.05, 'Contig0_d', 'Contig2_d']
[1, 1383, 1253, 2603, 1383, 1351, 82.39, 'Read0_d', 'Read1705_p']
[1, 718, 4334, 5074, 718, 741, 91.91, 'Contig0_d', 'Read1018_d']
'''
# print dataListCC[0]
# print dataListRR[0]
# print dataListCR[0]
# for eachitem in dataListCC:
# print eachitem
addDataToList(dataListCC, G, 0, 0, 'C', 'C')
# for eachitem in dataListRR[0:10]:
# print eachitem , lenDicRR[eachitem[-2]], lenDicRR[eachitem[-1]]
addDataToList(dataListRR, G, N1, N1, 'R', 'R')
addDataToList(dataListCR, G, 0, N1, 'C', 'R')
# G.reportEdge()
G.saveToFile(folderName, graphName)
checkGraphLength(G, N1, lenDicRR)
# print len(G.graphNodesList[0].listOfPrevNodes), len(G.graphNodesList[0].listOfNextNodes)
print "len(G.graphNodesList)", len(G.graphNodesList)
def resolvingTandem(
folderName, mummerPath, contigReadGraph, contigFilename, readsetFilename, optTypeFileHeader, repeatSpec
):
print "resolvingTandem"
"""
Input : repeat info
Output : count, join.
Algorithm:
1. Find loops
2. Form repeat
3. Form chain of repeat copies back to back
4. Align reads
5. Calculate extra bases beyond flanking region
6. Calculate count
7. Join the contigs
"""
# 0 ) Load all the data
thres = 5
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
lenDicCC = IORobot.obtainLength(folderName, contigFilename + "_Double.fasta")
N1 = len(lenDicCC)
maxDuplicate = 10
repeatTempFilename = "tandemRepeatTemplate.fasta"
mummerFile = "myTandemRepeatTemplate"
myContigsDic = IORobot.loadContigsFromFile(folderName, readsetFilename + "_Double.fasta")
lenDicRR = IORobot.obtainLength(folderName, readsetFilename + "_Double.fasta")
header = optTypeFileHeader + "RR"
dataListRR = alignerRobot.extractMumData(folderName, header + "Out")
dataListRR = abunHouseKeeper.filterData(dataListRR, lenDicRR)
dataListRRDic = {}
for eachitem in dataListRR:
if eachitem[2] < thres:
dataListRRDic[eachitem[-2] + ";" + eachitem[-1]] = eachitem[4]
header = optTypeFileHeader + "CR"
lenDicCC = IORobot.obtainLength(folderName, contigFilename + "_Double.fasta")
lenDicCR = dict(lenDicCC.items() + lenDicRR.items())
dataListCR = alignerRobot.extractMumData(folderName, header + "Out")
dataListCR = abunHouseKeeper.filterData(dataListCR, lenDicCR)
dataListCRDic = {}
for eachitem in dataListCR:
if eachitem[2] < thres:
dataListCRDic[eachitem[-2] + ";" + eachitem[-1]] = eachitem[4]
print dataListCRDic
json_data = open(folderName + repeatSpec, "r")
loadData = json.load(json_data)
contigsTmp = IORobot.loadContigsFromFile(folderName, contigFilename + "_Double.fasta")
readTmp = IORobot.loadContigsFromFile(folderName, readsetFilename + "_Double.fasta")
happyTandemList = {}
for eachrepProfile in loadData:
# 1)
startContig = eachrepProfile[-1][0][0]
isTerminate, returnPathList = DFSwithPath(G, G.graphNodesList[startContig], [startContig], N1, False)
# 2)
if isTerminate:
v = returnPathList[-1]
i = 0
tandemPath = []
while i < len(returnPathList):
if returnPathList[i] == v:
tandemPath = returnPathList[i:]
i = len(returnPathList)
i = i + 1
print returnPathList
print tandemPath
# 3) [fix it when have time later ; to just use graph; bug at the min thing]
repeatContent = ""
for kk in range(len(tandemPath[0:-1])):
eachitem = tandemPath[kk] - N1
nextitem = tandemPath[kk + 1] - N1
readName = "Read" + str(eachitem / 2) + "_"
nextReadName = "Read" + str(nextitem / 2) + "_"
if eachitem % 2 == 0:
readName = readName + "p"
elif eachitem % 2 == 1:
readName = readName + "d"
if nextitem % 2 == 0:
nextReadName = nextReadName + "p"
elif nextitem % 2 == 1:
nextReadName = nextReadName + "d"
overlap = dataListRRDic[readName + ";" + nextReadName]
print overlap
repeatContent = repeatContent + myContigsDic[readName][0:-overlap]
print "len(repeatContent)", len(repeatContent)
fout = open(folderName + repeatTempFilename, "w")
fout.write(">RepeatSegment\n")
repeatContentLarge = ""
for i in range(maxDuplicate):
fout.write(repeatContent)
repeatContentLarge = repeatContentLarge + repeatContent
fout.close()
# 4)
repeatReadList = eachrepProfile[1]
myList = []
for eachitem in repeatReadList:
readName = "Read" + str((eachitem - N1) / 2) + "_"
if eachitem % 2 == 0:
readName = readName + "p"
elif eachitem % 2 == 1:
readName = readName + "d"
myList.append(readName)
IORobot.putListToFileO(folderName, readsetFilename + "_Double.fasta", "toAlignReads", myList)
if True:
alignerRobot.useMummerAlign(mummerPath, folderName, mummerFile, repeatTempFilename, "toAlignReads.fasta")
dataList = alignerRobot.extractMumData(folderName, mummerFile + "Out")
# 5)
totalBasesMatch = 0
lrepeat = len(repeatContent)
c = findCoverageFromRawData(folderName)
# print "dataList[0]", dataList[0]
dataList.sort(key=itemgetter(-1))
for key, values in groupby(dataList, itemgetter(-1)):
maxValue = -1
for eachsub in values:
if eachsub[5] > maxValue:
maxValue = eachsub[5]
# print key, maxValue
totalBasesMatch = totalBasesMatch + maxValue
print c, lrepeat, totalBasesMatch
ct = totalBasesMatch * 1.0 / (c * lrepeat)
print "BIG NUMBER of THE DAY: ", ct
# 6)
# a) find the starting point
startContig = eachrepProfile[-1][0][0]
firstRead = eachrepProfile[-1][0][1] - N1
contigName = "Contig" + str(startContig / 2)
if startContig % 2 == 0:
contigName = contigName + "_p"
elif startContig % 2 == 1:
contigName = contigName + "_d"
readName = "Read" + str(firstRead / 2)
if firstRead % 2 == 0:
readName = readName + "_p"
elif firstRead % 2 == 1:
readName = readName + "_d"
overlapFirst = dataListCRDic[contigName + ";" + readName]
tmpCombine = contigsTmp[contigName][0:-overlapFirst] + readTmp[readName]
f1 = open(folderName + "firstOverlap.fasta", "w")
f1.write(">combined\n")
f1.write(tmpCombine)
f1.close()
if True:
alignerRobot.useMummerAlign(
mummerPath, folderName, "myFirstOverlap", repeatTempFilename, "firstOverlap.fasta"
)
dataList = alignerRobot.extractMumData(folderName, "myFirstOverlap" + "Out")
dataList.sort(key=itemgetter(0))
maxVal = -1
maxItm = []
for eachi in dataList:
if eachi[5] > maxVal:
maxVal = eachi[5]
maxItm = eachi
print maxItm
if len(maxItm) > 0:
repeatStart = maxItm[0]
contigEnd = maxItm[2]
else:
repeatStart = 0
contigEnd = -1
# b) format return : prepare the repeat template
print "ct*lrepeat", int(repeatStart + ct * lrepeat)
print "repeatStart", repeatStart
happyTandemList[contigName] = repeatContentLarge[repeatStart : int(repeatStart + ct * lrepeat)]
contigsTmp[contigName] = tmpCombine[0:contigEnd]
print "len(contigsTmp[contigName])", len(contigsTmp[contigName])
print "len(happyTandemList[contigName])", len(happyTandemList[contigName])
# 7) Combine all the repeat information and do the join
leaderList = [i for i in range(len(contigsTmp))]
for eachrepProfile in loadData:
startContig = eachrepProfile[-1][0][0]
endContig = eachrepProfile[-1][-1][-1]
leaderContig = leaderList[startContig]
leaderName = parseIDToName(leaderContig)
endName = parseIDToName(endContig)
startName = parseIDToName(startContig)
contigsTmp[leaderName] = contigsTmp[leaderName] + happyTandemList[startName]
if endContig != leaderContig:
contigsTmp[leaderName] = contigsTmp[leaderName] + contigsTmp[endName]
contigsTmp[endName] = ""
leaderList[endContig] = leaderContig
leaderAgg = [[] for i in range(len(leaderList))]
for i in range(len(leaderList)):
leaderAgg[leaderList[i]].append(i)
checkingList = [False for i in range(N1)]
fout = open(folderName + "tademResolved.fasta", "w")
counter = 0
for eachcontig in contigsTmp:
id = abunHouseKeeper.parseEdgeNameToID(eachcontig, "C")
if checkingList[id / 2] == False:
fout.write(">Segkk" + str(counter) + "\n")
fout.write(contigsTmp[eachcontig])
counter = counter + 1
for eachkk in leaderAgg[leaderList[id]]:
checkingList[eachkk / 2] = True
fout.close()
def getAllAssociatedReads(folderName, mummerLink,forFastaName):
'''
Input : relatedReads.fasta, raw_reads.fasta
Output : all_associated_reads.fasta
Algorithm :
a) Get all the associated reads
b) Loop for N=1 times : ==> this correspond 4 reads to link between the bridge in total
i) Align the raws and tmp_seedReads
ii) Put the new reads into the SeedReads
'''
header, referenceFile, queryFile = "seedReads", forFastaName + ".fasta" , "raw_reads.fasta"
command = "cp " + folderName + "relatedReads.fasta " + folderName + referenceFile
os.system(command)
N = abunHouseKeeper.abunGlobalReadSearchDepth
print "N: ", N
if N >0 :
for trial in range(N):
print "trial", trial
numberOfFiles = 20
if True:
workerList = []
for dummyI in range(1, numberOfFiles + 1):
indexOfMum = ""
if dummyI < 10:
indexOfMum = "0" + str(dummyI)
else:
indexOfMum = str(dummyI)
outputName, referenceName, queryName, specialName= header+indexOfMum, referenceFile, "raw_reads.part-"+ indexOfMum + ".fasta", header + indexOfMum
workerList.append([outputName, referenceName, queryName, specialName])
alignerRobot.useMummerAlignBatch(mummerLink, folderName, workerList, houseKeeper.globalParallel ,False)
dataList = []
for i in range(1, 1+numberOfFiles):
if i < 10:
indexOfMum = "0" + str(i)
else:
indexOfMum = str(i)
dataList = dataList+ alignerRobot.extractMumData(folderName, header+ str(indexOfMum)+"Out")
filterList = []
lenDicRR = IORobot.obtainLength(folderName, queryFile)
print "len(dataList)", len(dataList)
for eachitem in dataList:
if checkSatisfy(eachitem, lenDicRR):
filterList.append(eachitem)
filterList.sort(key=itemgetter(-1))
newReads = []
for key, items in groupby(filterList, itemgetter(-1)):
newReads.append(key)
f = open(folderName + forFastaName + ".txt", 'w')
for eachitem in newReads:
f.write(eachitem + "\n")
f.close()
command = "perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' " + folderName + forFastaName + ".txt " + folderName + "raw_reads.fasta > " + folderName + forFastaName + ".fasta"
os.system(command)
else:
os.system("cp " + folderName + "relatedReads.fasta " + folderName + forFastaName + ".fasta")
def resolvingTandem(folderName, mummerPath, contigReadGraph,contigFilename, readsetFilename, optTypeFileHeader, repeatSpec):
print "resolvingTandem"
'''
Input : repeat info
Output : count, join.
Algorithm:
1. Find loops
2. Form repeat
3. Form chain of repeat copies back to back
4. Align reads
5. Calculate extra bases beyond flanking region
6. Calculate count
7. Join the contigs
'''
# 0 ) Load all the data
thres = 5
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
lenDicCC = IORobot.obtainLength(folderName, contigFilename+"_Double.fasta")
N1 = len(lenDicCC)
maxDuplicate = 10
repeatTempFilename = "tandemRepeatTemplate.fasta"
mummerFile = "myTandemRepeatTemplate"
myContigsDic = IORobot.loadContigsFromFile(folderName, readsetFilename+"_Double.fasta")
lenDicRR = IORobot.obtainLength(folderName, readsetFilename + "_Double.fasta")
header = optTypeFileHeader + "RR"
dataListRR = alignerRobot.extractMumData(folderName, header + "Out")
dataListRR = abunHouseKeeper.filterData(dataListRR, lenDicRR)
dataListRRDic = {}
for eachitem in dataListRR:
if eachitem[2] < thres:
dataListRRDic[eachitem[-2] +";"+eachitem[-1]] = eachitem[4]
header = optTypeFileHeader + "CR"
lenDicCC = IORobot.obtainLength(folderName, contigFilename + "_Double.fasta")
lenDicCR = dict(lenDicCC.items() + lenDicRR.items())
dataListCR = alignerRobot.extractMumData(folderName, header + "Out")
dataListCR = abunHouseKeeper.filterData(dataListCR, lenDicCR)
dataListCRDic = {}
for eachitem in dataListCR:
if eachitem[2] < thres:
dataListCRDic[eachitem[-2] +";"+eachitem[-1]] = eachitem[4]
print dataListCRDic
json_data = open(folderName + repeatSpec, 'r')
loadData = json.load(json_data)
contigsTmp = IORobot.loadContigsFromFile(folderName, contigFilename+"_Double.fasta")
readTmp = IORobot.loadContigsFromFile(folderName, readsetFilename + "_Double.fasta")
happyTandemList = {}
for eachrepProfile in loadData:
# 1)
startContig = eachrepProfile[-1][0][0]
isTerminate, returnPathList = DFSwithPath(G, G.graphNodesList[startContig], [startContig], N1, False)
# 2)
if isTerminate:
v = returnPathList[-1]
i =0
tandemPath = []
while i < len(returnPathList):
if returnPathList[i] == v:
tandemPath = returnPathList[i:]
i = len(returnPathList)
i = i +1
print returnPathList
print tandemPath
# 3) [fix it when have time later ; to just use graph; bug at the min thing]
repeatContent = ""
for kk in range(len(tandemPath[0:-1])):
eachitem = tandemPath[kk]- N1
nextitem = tandemPath[kk+1] - N1
readName = "Read" + str(eachitem/2) + "_"
nextReadName = "Read" + str(nextitem/2) + "_"
if eachitem %2 ==0 :
readName = readName + "p"
elif eachitem %2 ==1:
readName = readName + "d"
if nextitem %2 ==0 :
nextReadName = nextReadName + "p"
elif nextitem %2 ==1:
nextReadName = nextReadName + "d"
overlap = dataListRRDic[readName + ";" + nextReadName]
print overlap
repeatContent = repeatContent + myContigsDic[readName][0:-overlap]
print "len(repeatContent)", len(repeatContent)
fout = open(folderName + repeatTempFilename, 'w')
fout.write(">RepeatSegment\n")
repeatContentLarge = ""
for i in range(maxDuplicate):
fout.write(repeatContent)
repeatContentLarge= repeatContentLarge + repeatContent
fout.close()
# 4)
repeatReadList = eachrepProfile[1]
myList= []
for eachitem in repeatReadList:
readName = "Read" + str((eachitem- N1)/2) + "_"
if eachitem %2 ==0 :
readName = readName + "p"
elif eachitem %2 ==1:
readName = readName + "d"
myList.append(readName)
IORobot.putListToFileO(folderName, readsetFilename+"_Double.fasta", "toAlignReads", myList)
if True:
alignerRobot.useMummerAlign(mummerPath, folderName,mummerFile , repeatTempFilename, "toAlignReads.fasta")
dataList = alignerRobot.extractMumData(folderName, mummerFile+"Out")
# 5)
totalBasesMatch = 0
lrepeat = len(repeatContent)
c = findCoverageFromRawData(folderName)
# print "dataList[0]", dataList[0]
dataList.sort(key = itemgetter(-1))
for key, values in groupby(dataList,itemgetter(-1)):
maxValue = -1
for eachsub in values:
if eachsub[5] > maxValue:
maxValue = eachsub[5]
#print key, maxValue
totalBasesMatch = totalBasesMatch + maxValue
print c, lrepeat, totalBasesMatch
ct = totalBasesMatch*1.0/(c*lrepeat)
print "BIG NUMBER of THE DAY: ", ct
# 6)
# a) find the starting point
startContig = eachrepProfile[-1][0][0]
firstRead = eachrepProfile[-1][0][1]-N1
contigName = "Contig"+ str(startContig/2)
if startContig %2 == 0:
contigName = contigName + "_p"
elif startContig%2 ==1:
contigName = contigName + "_d"
readName = "Read"+ str(firstRead/2)
if firstRead %2 == 0:
readName = readName + "_p"
elif firstRead%2 ==1:
readName = readName + "_d"
overlapFirst = dataListCRDic[contigName+";"+readName]
tmpCombine = contigsTmp[contigName][0:-overlapFirst] + readTmp[readName]
f1 = open(folderName + "firstOverlap.fasta", 'w')
f1.write(">combined\n")
f1.write(tmpCombine)
f1.close()
if True:
alignerRobot.useMummerAlign(mummerPath, folderName,"myFirstOverlap" , repeatTempFilename, "firstOverlap.fasta")
dataList = alignerRobot.extractMumData(folderName, "myFirstOverlap"+"Out")
dataList.sort(key = itemgetter(0))
maxVal = -1
maxItm = []
for eachi in dataList:
if eachi[5] > maxVal:
maxVal = eachi[5]
maxItm = eachi
print maxItm
if len(maxItm) > 0 :
repeatStart = maxItm[0]
contigEnd = maxItm[2]
else:
repeatStart = 0
contigEnd = -1
# b) format return : prepare the repeat template
print "ct*lrepeat", int(repeatStart + ct*lrepeat)
print "repeatStart", repeatStart
happyTandemList[contigName]= repeatContentLarge[repeatStart:int(repeatStart + ct*lrepeat)]
contigsTmp[contigName] = tmpCombine[0:contigEnd]
print "len(contigsTmp[contigName])", len(contigsTmp[contigName])
print "len(happyTandemList[contigName])", len(happyTandemList[contigName])
# 7) Combine all the repeat information and do the join
leaderList = [i for i in range(len(contigsTmp))]
for eachrepProfile in loadData:
startContig = eachrepProfile[-1][0][0]
endContig = eachrepProfile[-1][-1][-1]
leaderContig = leaderList[startContig]
leaderName = parseIDToName(leaderContig)
endName = parseIDToName(endContig)
startName = parseIDToName(startContig)
contigsTmp[leaderName] = contigsTmp[leaderName] + happyTandemList[startName]
if endContig != leaderContig:
contigsTmp[leaderName] = contigsTmp[leaderName] + contigsTmp[endName]
contigsTmp[endName] = ""
leaderList[endContig] = leaderContig
leaderAgg = [[] for i in range(len(leaderList))]
for i in range(len(leaderList)):
leaderAgg[leaderList[i]].append(i)
checkingList = [False for i in range(N1)]
fout = open(folderName + "tademResolved.fasta", 'w')
counter = 0
for eachcontig in contigsTmp:
id = abunHouseKeeper.parseEdgeNameToID(eachcontig, 'C')
if checkingList[id/2] == False:
fout.write(">Segkk"+str(counter)+ "\n")
fout.write(contigsTmp[eachcontig])
counter = counter + 1
for eachkk in leaderAgg[leaderList[id]]:
checkingList[eachkk/2] = True
fout.close()
def formReadContigStringGraph(folderName, mummerLink, contigFilename,
readsetFilename, optTypeFileHeader, graphName):
'''
Input : all_associated_reads.fasta, improved3.fasta
Output : (G) String Graph linking the reads and contigs
Algorithm:
a) Form double reads and contigs V
b) Mummer the data and extract dataList three times V
c) Use the subroutine to output a graph V
d) Output the graph to a file phasing_String_graph.graph V
'''
G = []
IORobot.writeToFile_Double1(folderName, contigFilename + ".fasta",
contigFilename + "_Double.fasta", "contig")
IORobot.writeToFile_Double1(folderName, readsetFilename + ".fasta",
readsetFilename + "_Double.fasta", "reads")
header, referenceFile, queryFile = optTypeFileHeader + "CC", contigFilename + "_Double.fasta", contigFilename + "_Double.fasta"
if True:
alignerRobot.useMummerAlign(mummerLink, folderName, header,
referenceFile, queryFile)
lenDicCC = IORobot.obtainLength(folderName,
contigFilename + "_Double.fasta")
dataListCC = alignerRobot.extractMumData(folderName, header + "Out")
dataListCC = abunHouseKeeper.filterData(dataListCC, lenDicCC)
header, referenceFile, queryFile = optTypeFileHeader + "RR", readsetFilename + "_Double.fasta", readsetFilename + "_Double.fasta"
lenDicRR = IORobot.obtainLength(folderName,
readsetFilename + "_Double.fasta")
if not abunHouseKeeper.abunGlobalRRDisable:
if True:
alignerSubRoutine(folderName, referenceFile, queryFile, mummerLink,
header)
dataListRR = alignerRobot.extractMumData(folderName, header + "Out")
dataListRR = abunHouseKeeper.filterData(dataListRR, lenDicRR)
for eachitem in dataListRR:
if eachitem[-2] == "Read164_p" and eachitem[-1] == "Read159_p":
print "debug", eachitem
if eachitem[-1] == "Read164_p" and eachitem[-2] == "Read159_p":
print "debug", eachitem
dataListRR = abunHouseKeeper.filterDataIdentical(dataListRR, lenDicRR)
else:
dataListRR = []
header, referenceFile, queryFile = optTypeFileHeader + "CR", contigFilename + "_Double.fasta", readsetFilename + "_Double.fasta"
if True:
alignerSubRoutine(folderName, referenceFile, queryFile, mummerLink,
header)
#alignerRobot.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile)
lenDicCR = dict(lenDicCC.items() + lenDicRR.items())
dataListCR = alignerRobot.extractMumData(folderName, header + "Out")
dataListCR = abunHouseKeeper.filterData(dataListCR, lenDicCR)
numberOfNodes = len(lenDicCR)
G = graphLib.seqGraph(numberOfNodes)
N1, N2 = len(lenDicCC), len(lenDicRR)
print "N1, N2, numberOfNodes: ", N1, N2, numberOfNodes
'''
e.g. of dataListCC[0], dataListRR[0], dataListCR[0]
[1, 520, 2913194, 2913716, 520, 523, 99.05, 'Contig0_d', 'Contig2_d']
[1, 1383, 1253, 2603, 1383, 1351, 82.39, 'Read0_d', 'Read1705_p']
[1, 718, 4334, 5074, 718, 741, 91.91, 'Contig0_d', 'Read1018_d']
'''
# print dataListCC[0]
# print dataListRR[0]
# print dataListCR[0]
# for eachitem in dataListCC:
# print eachitem
addDataToList(dataListCC, G, 0, 0, 'C', 'C')
# for eachitem in dataListRR[0:10]:
# print eachitem , lenDicRR[eachitem[-2]], lenDicRR[eachitem[-1]]
addDataToList(dataListRR, G, N1, N1, 'R', 'R')
addDataToList(dataListCR, G, 0, N1, 'C', 'R')
# G.reportEdge()
G.saveToFile(folderName, graphName)
checkGraphLength(G, N1, lenDicRR)
# print len(G.graphNodesList[0].listOfPrevNodes), len(G.graphNodesList[0].listOfNextNodes)
print "len(G.graphNodesList)", len(G.graphNodesList)
def generateAbundanceGraph(folderName, mummerLink):
print "generateAbundanceGraph"
'''
1. Find your favorite mappers to map read back
a. MUMmer, Bowtie, bbmap, any that works V
b. And then write a short parser to parse the results V
'''
numberOfFiles = 20
workerList = []
for dummyI in range(1, numberOfFiles + 1):
indexOfMum = ""
if dummyI < 10:
indexOfMum = "0" + str(dummyI)
else:
indexOfMum = str(dummyI)
'''
"outGapFillRefine"+indexOfMum , "smaller_improvedContig.fasta", "relatedReads_Double.part-" + indexOfMum + ".fasta", "fromMumRefine" + indexOfMum
'''
outputName, referenceName, queryName, specialName= "outAbun"+indexOfMum, "improved3.fasta", "raw_reads.part-"+ indexOfMum + ".fasta", "outAbun" + indexOfMum
workerList.append([outputName, referenceName, queryName, specialName])
if True:
alignerRobot.useMummerAlignBatch(mummerLink, folderName, workerList, houseKeeper.globalParallel ,False)
'''
command = mummerLink + "nucmer --maxmatch --nosimplify -p " + folderName + "out " + folderName + "improved3.fasta "+folderName+"raw_reads.part-" + indexOfMum + ".fasta"
os.system(command)
command = mummerLink + "show-coords -r " + folderName + "out.delta > " + folderName + "fromMumAbun" + indexOfMum
os.system(command)
'''
dataList = []
for i in range(1, 1+numberOfFiles):
if i < 10:
indexOfMum = "0" + str(i)
else:
indexOfMum = str(i)
dataList = dataList+ alignerRobot.extractMumData(folderName, "outAbun"+ str(indexOfMum)+"Out")
'''
2. Calculate count on the abundances
a. Aggregate by taking average [put weights on bin along contigs]
b. Inheritance and a subclass
'''
lenDic = IORobot.obtainLength(folderName, "improved3.fasta")
readLenDic = IORobot.obtainLength(folderName , "raw_reads.fasta")
myCountDic = {}
for eachitem in lenDic:
myCountDic[eachitem] = [0 for i in range(lenDic[eachitem])]
thres = 30
lenSum = 0
extraDataList= []
print "len(dataList)", len(dataList)
if not abunHouseKeeper.abunGlobalAvoidrefine:
myCountDic = evaluateCoverage(dataList, lenDic, readLenDic, folderName, mummerLink, True)
extraDataList = alignerRobot.extractMumData(folderName, "abunMissOut" )
else:
extraDataList = []
dataList = dataList + extraDataList
myCountDic = evaluateCoverage(dataList, lenDic, readLenDic, folderName, mummerLink,False)
with open(folderName + 'myCountDic.json', 'w') as f:
json.dump(myCountDic, f)
return myCountDic
