def tryToFusion(fastqSequence, reverseFileName, threshold, log, seqOutput):
fastqSequence.applyDrasticThreshold(threshold)
f = open(reverseFileName, "r")
reverseLineHeader = fastqSequence.getReverseLineHeader()
logging.debug("Search " + reverseLineHeader)
lastHeaderLineNumber = 0
lastSeparatorLineNumber = 0
parseFastq = False
rFastqSequence = None
lineNumber = 0
for line in f:
line = line[:-1]
lineNumber += 1
#logging.debug(str(lineNumber) +"\t**** "+line + "\t" + str(line[0] == "@") + "\t" + str(lineNumber == 1))
if line[0] == "@" and (lastSeparatorLineNumber != lineNumber - 1 or lineNumber == 1):
logging.debug(line + " est un header")
if parseFastq:
rFastqSequence.applyDrasticThreshold(threshold)
s = FastqSequence.matchFastqSequence(fastqSequence, rFastqSequence)
if s != None:
seqOutput.write(">" + s.getLineHeader() + "\n")
seqOutput.write(s.sequence + "\n")
logging.debug(s.getLineHeader() + "\t" + str(s.typeFusion))
if s.typeFusion == s.TYPE_FUSION_OK:
log.write("Merge " + fastqSequence.getLineHeader() + " with " + rFastqSequence.getLineHeader() + "\n")
elif s.typeFusion == s.TYPE_FUSION_NO_MATCH:
log.write("Forced merge " + fastqSequence.getLineHeader() + " with " + rFastqSequence.getLineHeader() + "\n")
elif s.typeFusion == s.TYPE_FUSION_PARTIAL:
log.write("Partial merge " + fastqSequence.getLineHeader() + " with " + rFastqSequence.getLineHeader() + "\n")
else:
log.write("Can't merge " + fastqSequence.getLineHeader() + " with " + rFastqSequence.getLineHeader() + "\n")
else:
log.write("*Can't merge " + fastqSequence.getLineHeader() + " with " + rFastqSequence.getLineHeader() + "\n")
parseFastq = False
#logging.debug("-"+line)
#logging.debug("-"+reverseLineHeader)
#logging.debug(line + " =?= " + reverseLineHeader + " ? " + str(line == reverseLineHeader))
if line == reverseLineHeader:
parseFastq = True
if parseFastq:
rFastqSequence = FastqSequence.readFasqSequenceHeader(line)
#logging.debug("Compare to " + rFastqSequence.getLineHeader())
lastHeaderLineNumber = lineNumber
elif parseFastq:
if lastHeaderLineNumber == lineNumber - 1:
rFastqSequence.setSequence(line)
elif line[0] == "+":
lastSeparatorLineNumber = lineNumber
elif lastSeparatorLineNumber == lineNumber - 1:
rFastqSequence.setQuality(line)
f.close()
def testQualityThreshold(fastqFileName, threshold):
f = open(fastqFileName, "r")
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)
avLen = len(fastqSequence.sequence)
fastqSequence.applyDrasticThreshold(threshold)
logger.debug("Avant : " + str(avLen) + " / Apres : " +
str(len(fastqSequence.sequence)))
fastqSequence = FastqSequence.readFasqSequenceHeader(line)
lastHeaderLineNumber = lineNumber
logging.debug(line)
elif lastHeaderLineNumber == lineNumber - 1:
fastqSequence.setSequence(line)
elif line[0] == "+":
lastSeparatorLineNumber = lineNumber
elif lastSeparatorLineNumber == lineNumber - 1:
fastqSequence.setQuality(line)
lineNumber += 1
#tryToFusion(fastqSequence, reverseFileName, threshold, log, seqOutput)
f.close()
def readFastQFile(fileName, reverseFileName, threshold, seqOutputName,
logFileName):
f = open(fileName, "r")
log = open(logFileName, "w")
seqOutput = open(seqOutputName, "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)
fastqSequence = FastqSequence.readFasqSequenceHeader(line)
lastHeaderLineNumber = lineNumber
logging.debug(line)
elif lastHeaderLineNumber == lineNumber - 1:
fastqSequence.setSequence(line)
elif line[0] == "+":
lastSeparatorLineNumber = lineNumber
elif lastSeparatorLineNumber == lineNumber - 1:
fastqSequence.setQuality(line)
lineNumber += 1
tryToFusion(fastqSequence, reverseFileName, threshold, log, seqOutput)
f.close()
log.close()
seqOutput.close()
def readFastQFile(fileName, reverseFileName, threshold, logFileName):
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)
fastqSequence = FastqSequence.readFasqSequenceHeader(line)
lastHeaderLineNumber = lineNumber
elif lastHeaderLineNumber == lineNumber - 1:
fastqSequence.setSequence(line)
elif line[0] == "+":
lastSeparatorLineNumber = lineNumber
elif lastSeparatorLineNumber == lineNumber - 1:
fastqSequence.setQuality(line)
lineNumber += 1
tryToFusion(fastqSequence, reverseFileName, threshold, log)
f.close()
log.close()
def testQualityThreshold(fastqFileName, threshold):
f = open(fastqFileName, "r")
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)
avLen = len(fastqSequence.sequence)
fastqSequence.applyDrasticThreshold(threshold)
logger.debug("Avant : " + str(avLen) + " / Apres : " + str(len(fastqSequence.sequence)))
fastqSequence = FastqSequence.readFasqSequenceHeader(line)
lastHeaderLineNumber = lineNumber
logging.debug(line)
elif lastHeaderLineNumber == lineNumber - 1:
fastqSequence.setSequence(line)
elif line[0] == "+":
lastSeparatorLineNumber = lineNumber
elif lastSeparatorLineNumber == lineNumber - 1:
fastqSequence.setQuality(line)
lineNumber += 1
#tryToFusion(fastqSequence, reverseFileName, threshold, log, seqOutput)
f.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 tryToFusion(fastqSequence, reverseFileName, threshold, log):
fastqSequence
f = open(reverseFileName, "r")
reverseLineHeader = fastqSequence.getReverseLineHeader()
lastHeaderLineNumber = 0
lastSeparatorLineNumber = 0
parseFastq = False
rFastqSequence = None
lineNumber = 0
for line in f:
line = line[:-1]
lineNumber += 1
if line[0] == "@" and lastSeparatorLineNumber != lineNumber - 1:
if parseFastq:
rFastqSequence.applyDrasticThreshold(threshold)
s = FastqSequence.matchFastqSequence(fastqSequence, rFastqSequence)
if s != None:
print(s.getLineHeader())
print(s.sequence)
else:
log.write("Can't merge " + fastqSequence.getLineHeader() + " with " + rFastqSequence.getLineHeader() + "\n")
parseFastq = False
if line == reverseLineHeader:
parseFastq = True
if parseFastq:
rFastqSequence = FastqSequence.readFasqSequenceHeader(line)
lastHeaderLineNumber = lineNumber
elif parseFastq:
if lastHeaderLineNumber == lineNumber - 1:
rFastqSequence.setSequence(line)
elif line[0] == "+":
lastSeparatorLineNumber = lineNumber
elif lastSeparatorLineNumber == lineNumber - 1:
rFastqSequence.setQuality(line)
f.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 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 tryToFusion(fastqSequence, reverseFileName, threshold, log, seqOutput):
fastqSequence.applyDrasticThreshold(threshold)
f = open(reverseFileName, "r")
reverseLineHeader = fastqSequence.getReverseLineHeader()
logging.debug("Search " + reverseLineHeader)
lastHeaderLineNumber = 0
lastSeparatorLineNumber = 0
parseFastq = False
rFastqSequence = None
lineNumber = 0
for line in f:
line = line[:-1]
lineNumber += 1
#logging.debug(str(lineNumber) +"\t**** "+line + "\t" + str(line[0] == "@") + "\t" + str(lineNumber == 1))
if line[0] == "@" and (lastSeparatorLineNumber != lineNumber - 1
or lineNumber == 1):
logging.debug(line + " est un header")
if parseFastq:
rFastqSequence.applyDrasticThreshold(threshold)
s = FastqSequence.matchFastqSequence(fastqSequence,
rFastqSequence)
if s != None:
seqOutput.write(">" + s.getLineHeader() + "\n")
seqOutput.write(s.sequence + "\n")
logging.debug(s.getLineHeader() + "\t" + str(s.typeFusion))
if s.typeFusion == s.TYPE_FUSION_OK:
log.write("Merge " + fastqSequence.getLineHeader() +
" with " + rFastqSequence.getLineHeader() +
"\n")
elif s.typeFusion == s.TYPE_FUSION_NO_MATCH:
log.write("Forced merge " +
fastqSequence.getLineHeader() + " with " +
rFastqSequence.getLineHeader() + "\n")
elif s.typeFusion == s.TYPE_FUSION_PARTIAL:
log.write("Partial merge " +
fastqSequence.getLineHeader() + " with " +
rFastqSequence.getLineHeader() + "\n")
else:
log.write("Can't merge " +
fastqSequence.getLineHeader() + " with " +
rFastqSequence.getLineHeader() + "\n")
else:
log.write("*Can't merge " + fastqSequence.getLineHeader() +
" with " + rFastqSequence.getLineHeader() + "\n")
parseFastq = False
#logging.debug("-"+line)
#logging.debug("-"+reverseLineHeader)
#logging.debug(line + " =?= " + reverseLineHeader + " ? " + str(line == reverseLineHeader))
if line == reverseLineHeader:
parseFastq = True
if parseFastq:
rFastqSequence = FastqSequence.readFasqSequenceHeader(line)
#logging.debug("Compare to " + rFastqSequence.getLineHeader())
lastHeaderLineNumber = lineNumber
elif parseFastq:
if lastHeaderLineNumber == lineNumber - 1:
rFastqSequence.setSequence(line)
elif line[0] == "+":
lastSeparatorLineNumber = lineNumber
elif lastSeparatorLineNumber == lineNumber - 1:
rFastqSequence.setQuality(line)
f.close()