def writeToFile_Double1(folderName, fileName1, fileName2, option="contig"):
f2 = open(folderName + fileName2, 'w')
fOriginal = open(folderName + fileName1, '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)
print "len(readSet)", len(readSet)
fOriginal.close()
if option == "contig":
header = ">Contig"
else:
header = ">Read"
for eachcontig, dum in zip(readSet, range(len(readSet))):
f2.write(header + str(dum) + "_p\n")
f2.write(eachcontig + '\n')
f2.write(header + str(dum) + "_d\n")
f2.write(houseKeeper.reverseComplement(eachcontig) + '\n')
f2.close()
def writeToFile_Double1(folderName, fileName1, fileName2, option="contig"):
f2 = open(folderName + fileName2, 'w')
fOriginal = open(folderName + fileName1, '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)
print "len(readSet)", len(readSet)
fOriginal.close()
if option == "contig":
header = ">Contig"
else:
header = ">Read"
for eachcontig, dum in zip(readSet, range(len(readSet))):
f2.write(header + str(dum) + "_p\n")
f2.write(eachcontig + '\n')
f2.write(header + str(dum) + "_d\n")
f2.write(houseKeeper.reverseComplement(eachcontig) + '\n')
f2.close()
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()