def newPipeline():
checkArgumentMarkerReducer()
m = DnaUtils.readIUPACFile(sys.argv[1])
mapOligos = DnaUtils.readOligosFile(sys.argv[2], m)
# for k in mapOligos:
# for e in mapOligos[k]:
# print(e)
# sys.exit(1)
readSingleFastQFile(sys.argv[4], 10, "log.txt", mapOligos, sys.argv[3])
def newPipeline():
checkArgumentMarkerReducer()
m = DnaUtils.readIUPACFile(sys.argv[1])
mapOligos = DnaUtils.readOligosFile(sys.argv[2], m)
# for k in mapOligos:
# for e in mapOligos[k]:
# print(e)
# sys.exit(1)
readSingleFastQFile(sys.argv[4], 10, "log.txt", mapOligos, sys.argv[3])
def setSequence(self, value, forced=False):
if forced:
self.sequence = value
else:
if self.readDirection == FastqSequence.READ_DIRECTION_LEFT_TO_RIGHT:
self.sequence = value
else:
self.sequence = DnaUtils.complementAndReverseDnaSequence(value)
self.logger.debug("self.sequence : " + self.sequence)
def setSequence(self, value, forced=False):
if forced:
self.sequence = value
else:
if self.readDirection == FastqSequence.READ_DIRECTION_LEFT_TO_RIGHT:
self.sequence = value
else:
self.sequence = DnaUtils.complementAndReverseDnaSequence(value)
self.logger.debug("self.sequence : " + self.sequence)
def readSingleFastQFile(fileName, threshold, logFileName, mapOligos,
outputDir):
f = open(fileName, "r")
log = open(logFileName, "w")
lineNumber = 0
lastHeaderLineNumber = 0
lastSeparatorLineNumber = 0
sequences = []
fastqSequence = None
for line in f:
line = line[:-1]
if line[0] == "@" and lastSeparatorLineNumber != lineNumber - 1:
if fastqSequence != None:
#tryToFusion(fastqSequence, reverseFileName, threshold, log, seqOutput)
logger.debug("before threshold " + fastqSequence.sequence)
fastqSequence.applyDrasticThreshold(threshold)
logger.debug("after threshold " + fastqSequence.sequence)
logger.debug("after threshold " +
DnaUtils.complementAndReverseDnaSequence(
fastqSequence.sequence))
DnaUtils.splitMarker1(mapOligos, outputDir, fastqSequence,
fileName)
fastqSequence = FastqSequence.readFasqSequenceHeader(line)
lastHeaderLineNumber = lineNumber
logging.debug(line)
elif lastHeaderLineNumber == lineNumber - 1:
logging.debug("seq in file : " + line)
fastqSequence.setSequence(line)
elif line[0] == "+":
lastSeparatorLineNumber = lineNumber
elif lastSeparatorLineNumber == lineNumber - 1:
fastqSequence.setQuality(line)
lineNumber += 1
#tryToFusion(fastqSequence, reverseFileName, threshold, log, seqOutput)
fastqSequence.applyDrasticThreshold(threshold)
DnaUtils.splitMarker1(mapOligos, outputDir, fastqSequence, fileName)
f.close()
log.close()
def readSingleFastQFile(fileName, threshold, logFileName, mapOligos, outputDir):
f = open(fileName, "r")
log = open(logFileName, "w")
lineNumber = 0
lastHeaderLineNumber = 0
lastSeparatorLineNumber = 0
sequences = []
fastqSequence = None
for line in f:
line = line[:-1]
if line[0] == "@" and lastSeparatorLineNumber != lineNumber - 1:
if fastqSequence != None:
#tryToFusion(fastqSequence, reverseFileName, threshold, log, seqOutput)
logger.debug("before threshold " + fastqSequence.sequence)
fastqSequence.applyDrasticThreshold(threshold)
logger.debug("after threshold " + fastqSequence.sequence)
logger.debug("after threshold " + DnaUtils.complementAndReverseDnaSequence(fastqSequence.sequence))
DnaUtils.splitMarker1(mapOligos, outputDir, fastqSequence, fileName)
fastqSequence = FastqSequence.readFasqSequenceHeader(line)
lastHeaderLineNumber = lineNumber
logging.debug(line)
elif lastHeaderLineNumber == lineNumber - 1:
logging.debug("seq in file : " + line)
fastqSequence.setSequence(line)
elif line[0] == "+":
lastSeparatorLineNumber = lineNumber
elif lastSeparatorLineNumber == lineNumber - 1:
fastqSequence.setQuality(line)
lineNumber += 1
#tryToFusion(fastqSequence, reverseFileName, threshold, log, seqOutput)
fastqSequence.applyDrasticThreshold(threshold)
DnaUtils.splitMarker1(mapOligos, outputDir, fastqSequence, fileName)
f.close()
log.close()
def cutFusionAndMerge(headerF, dataF, headerR, dataR, wellThresholds, log,
outputFile):
logger.debug("[cutFusionAndMerge] " + headerF + ", " + headerR + ", " +
str(wellThresholds))
forward = 0
reverse = 1
dataF = dataF[0:wellThresholds[forward]]
#a = "ATAACGCTGTTATCCCTGCGGTAACTTGTTCTTTTGATCACTGTAAGTGGATCACACCTTCATTTTTATGATTTAAGAAAAACAATTCTTTTATTTTAGGTTAATATAACCATATAGTAGCGGAGGATTTTCTTTCTCCGGGATTGCCCCAATCAAAGCTTGTTTCAATTTGCCATGCTCTAGGCCTACTATTTCTATTATATTAGTTAGGGCTAATAGTAAATAACAATTAAAATTCAACTACAGCTCG"
#dataR = DnaUtils.complementAndReverseDnaSequence(dataR[0:wellThresholds[reverse]])
cdataR = DnaUtils.complementAndReverseDnaSequence(dataR)
cdataR = cdataR[:wellThresholds[reverse]]
#cdataR = DnaUtils.complementAndReverseDnaSequence(cdataR)
#data = merge(dataF, cdataR)
# print(dataF)
#print(DnaUtils.complementAndReverseDnaSequence(cdataR))
fastqSequenceForward = FastqSequence.createFasqSequenceHeader(headerF)
fastqSequenceForward.setSequence(dataF, True)
fastqSequenceForward.quality = None
fastqSequenceReverse = FastqSequence.createFasqSequenceHeader(headerR)
fastqSequenceReverse.setSequence(cdataR)
fastqSequenceReverse.quality = None
newFastQ = FastqSequence.matchFastqSequence(fastqSequenceForward,
fastqSequenceReverse)
logging.debug(newFastQ.getLineHeader() + "\t" + str(newFastQ.typeFusion))
if newFastQ.typeFusion == newFastQ.TYPE_FUSION_OK:
log.write("Merge " + fastqSequenceForward.getLineHeader() + " with " +
fastqSequenceReverse.getLineHeader() + "\n")
elif newFastQ.typeFusion == newFastQ.TYPE_FUSION_NO_MATCH:
log.write("Forced merge " + fastqSequenceForward.getLineHeader() +
" with " + fastqSequenceReverse.getLineHeader() + "\n")
elif newFastQ.typeFusion == newFastQ.TYPE_FUSION_PARTIAL:
log.write("Partial merge " + fastqSequenceForward.getLineHeader() +
" with " + fastqSequenceReverse.getLineHeader() + "\n")
else:
log.write("Can't merge " + fastqSequenceForward.getLineHeader() +
" with " + fastqSequenceReverse.getLineHeader() + "\n")
#outputFile.write(">" + newFastQ.getLineHeader() + "\n")
#outputFile.write(newFastQ.sequence + "\n")
#sys.exit(1)
return newFastQ
def cutFusionAndMerge(headerF, dataF, headerR, dataR, wellThresholds, log, outputFile):
logger.debug("[cutFusionAndMerge] " + headerF + ", " + headerR + ", " + str(wellThresholds))
forward = 0
reverse = 1
dataF = dataF[0:wellThresholds[forward]]
#a = "ATAACGCTGTTATCCCTGCGGTAACTTGTTCTTTTGATCACTGTAAGTGGATCACACCTTCATTTTTATGATTTAAGAAAAACAATTCTTTTATTTTAGGTTAATATAACCATATAGTAGCGGAGGATTTTCTTTCTCCGGGATTGCCCCAATCAAAGCTTGTTTCAATTTGCCATGCTCTAGGCCTACTATTTCTATTATATTAGTTAGGGCTAATAGTAAATAACAATTAAAATTCAACTACAGCTCG"
#dataR = DnaUtils.complementAndReverseDnaSequence(dataR[0:wellThresholds[reverse]])
cdataR = DnaUtils.complementAndReverseDnaSequence(dataR)
cdataR = cdataR[:wellThresholds[reverse]]
#cdataR = DnaUtils.complementAndReverseDnaSequence(cdataR)
#data = merge(dataF, cdataR)
# print(dataF)
#print(DnaUtils.complementAndReverseDnaSequence(cdataR))
fastqSequenceForward = FastqSequence.createFasqSequenceHeader(headerF)
fastqSequenceForward.setSequence(dataF, True)
fastqSequenceForward.quality = None
fastqSequenceReverse = FastqSequence.createFasqSequenceHeader(headerR)
fastqSequenceReverse.setSequence(cdataR)
fastqSequenceReverse.quality = None
newFastQ = FastqSequence.matchFastqSequence(fastqSequenceForward, fastqSequenceReverse)
logging.debug(newFastQ.getLineHeader() + "\t" + str(newFastQ.typeFusion))
if newFastQ.typeFusion == newFastQ.TYPE_FUSION_OK:
log.write("Merge " + fastqSequenceForward.getLineHeader() + " with " + fastqSequenceReverse.getLineHeader() + "\n")
elif newFastQ.typeFusion == newFastQ.TYPE_FUSION_NO_MATCH:
log.write("Forced merge " + fastqSequenceForward.getLineHeader() + " with " + fastqSequenceReverse.getLineHeader() + "\n")
elif newFastQ.typeFusion == newFastQ.TYPE_FUSION_PARTIAL:
log.write("Partial merge " + fastqSequenceForward.getLineHeader() + " with " + fastqSequenceReverse.getLineHeader() + "\n")
else:
log.write("Can't merge " + fastqSequenceForward.getLineHeader() + " with " + fastqSequenceReverse.getLineHeader() + "\n")
#outputFile.write(">" + newFastQ.getLineHeader() + "\n")
#outputFile.write(newFastQ.sequence + "\n")
#sys.exit(1)
return newFastQ
def generatePlot():
checkArgumentMarkerReducer()
logger.debug("IUPAC File : " + sys.argv[2])
iupacMap = DnaUtils.readIUPACFile(sys.argv[2])
logger.debug("forward MarkerMap File : " + sys.argv[3])
logger.debug("reverse MarkerMap File : " + sys.argv[4])
forwardMarkerMap = DnaUtils.readOligosFile(sys.argv[3], iupacMap)
reverseMarkerMap = DnaUtils.readOligosFile(sys.argv[4], iupacMap, True)
rAllOutputFileName = sys.argv[6] + ".r.csv"
fAllOutputFileName = sys.argv[6] + ".f.csv"
fAll = {}
rAll = {}
for root, dirs, files in os.walk(sys.argv[5]):
for f1le in files:
filePath = os.path.join(sys.argv[5], f1le)
logger.debug("file : " + filePath)
f, r = DnaUtils.readmarker(filePath, forwardMarkerMap,
reverseMarkerMap, sys.argv[6], False)
mergeMap(rAll, r)
mergeMap(fAll, f)
indexOsPath = filePath.rfind(os.sep)
if indexOsPath == -1:
indexOsPath = 0
else:
indexOsPath += 1
indexOfDot = filePath.rfind(".")
if indexOfDot == -1:
indexOfDot = len(filePath)
rOutputFileName = filePath[indexOsPath:indexOfDot] + ".r.csv"
fOutputFileName = filePath[indexOsPath:indexOfDot] + ".f.csv"
DnaUtils.mapToCsv(r, rOutputFileName)
DnaUtils.mapToCsv(f, fOutputFileName)
DnaUtils.mapToCsv(rAll, rAllOutputFileName)
DnaUtils.mapToCsv(fAll, fAllOutputFileName)
def setSequence(self, value):
if self.readDirection == FastqSequence.READ_DIRECTION_LEFT_TO_RIGHT:
self.sequence = value
else:
self.sequence = DnaUtils.complementAndReverseDnaSequence(value)
def generatePlot():
checkArgumentMarkerReducer()
logger.debug("IUPAC File : " + sys.argv[2])
iupacMap = DnaUtils.readIUPACFile(sys.argv[2])
logger.debug("forward MarkerMap File : " + sys.argv[3])
logger.debug("reverse MarkerMap File : " + sys.argv[4])
forwardMarkerMap = DnaUtils.readOligosFile(sys.argv[3], iupacMap)
reverseMarkerMap = DnaUtils.readOligosFile(sys.argv[4], iupacMap, True)
rAllOutputFileName = sys.argv[6] + ".r.csv"
fAllOutputFileName = sys.argv[6] + ".f.csv"
fAll = {}
rAll = {}
for root, dirs, files in os.walk(sys.argv[5]):
for f1le in files:
filePath = os.path.join(sys.argv[5], f1le)
logger.debug("file : " + filePath)
f,r = DnaUtils.readmarker(filePath, forwardMarkerMap, reverseMarkerMap, sys.argv[6], False)
mergeMap(rAll, r)
mergeMap(fAll, f)
indexOsPath = filePath.rfind(os.sep)
if indexOsPath == -1:
indexOsPath = 0
else:
indexOsPath += 1
indexOfDot = filePath.rfind(".")
if indexOfDot == -1:
indexOfDot = len(filePath)
rOutputFileName = filePath[indexOsPath:indexOfDot] + ".r.csv"
fOutputFileName = filePath[indexOsPath:indexOfDot] + ".f.csv"
DnaUtils.mapToCsv(r, rOutputFileName)
DnaUtils.mapToCsv(f, fOutputFileName)
DnaUtils.mapToCsv(rAll, rAllOutputFileName)
DnaUtils.mapToCsv(fAll, fAllOutputFileName)
