def evaluateReads(bam, referenceFile, bed, outputFile, mainOutput):
print("Run " + bam)
# Go through one chr after the other
testFile = SlamSeqBamFile(bam, referenceFile, None)
chromosomes = testFile.getChromosomes()
bedTree = bedToIntervallTree(bed)
#evalHist = [0] *
outFile = open(outputFile, "w")
print("read.name", "read.chromosome", "read.startRefPos", "sim.utr", "read.utr", "sim.tcCount", "read.tcCount", sep = "\t", file=outFile)
total = 0
correct = 0
correcPosWrongTC = 0
wrongPos = 0
minBaseQual = 0
for chromosome in chromosomes:
readIterator = testFile.readsInChromosome(chromosome, minBaseQual)
for read in readIterator:
total += 1
simInfo = read.name.split("_")
utrSim = simInfo[0]
tcCountSim = int(simInfo[2])
utrFound = None
if read.chromosome in bedTree:
overlaps = list(bedTree[read.chromosome][read.startRefPos:read.endRefPos])
if len(overlaps) > 0:
utrFound = overlaps[0].data
if utrFound == utrSim:
if tcCountSim == read.tcCount:
correct += 1
else:
correcPosWrongTC += 1
else:
wrongPos += 1
print(read.name, read.chromosome, read.startRefPos, utrSim, utrFound, tcCountSim, read.tcCount, sep = "\t", file=outFile)
print(correct * 100.0 / total, correcPosWrongTC * 100.0 / total, wrongPos * 100.0 / total, total)
def evaluateReads(bam, referenceFile, bed, outputFile, mainOutput):
print("Run " + bam)
# Go through one chr after the other
testFile = SlamSeqBamFile(bam, referenceFile, None)
chromosomes = testFile.getChromosomes()
bedTree = bedToIntervallTree(bed)
#evalHist = [0] *
outFile = open(outputFile, "w")
print("read.name",
"read.chromosome",
"read.startRefPos",
"sim.utr",
"read.utr",
"sim.tcCount",
"read.tcCount",
sep="\t",
file=outFile)
total = 0
correct = 0
correcPosWrongTC = 0
wrongPos = 0
minBaseQual = 0
for chromosome in chromosomes:
readIterator = testFile.readsInChromosome(chromosome, minBaseQual)
for read in readIterator:
total += 1
simInfo = read.name.split("_")
utrSim = simInfo[0]
tcCountSim = int(simInfo[2])
utrFound = None
if read.chromosome in bedTree:
overlaps = list(
bedTree[read.chromosome][read.startRefPos:read.endRefPos])
if len(overlaps) > 0:
utrFound = overlaps[0].data
if utrFound == utrSim:
if tcCountSim == read.tcCount:
correct += 1
else:
correcPosWrongTC += 1
else:
wrongPos += 1
print(read.name,
read.chromosome,
read.startRefPos,
utrSim,
utrFound,
tcCountSim,
read.tcCount,
sep="\t",
file=outFile)
#print(correct * 100.0 / total, correcPosWrongTC * 100.0 / total, wrongPos * 100.0 / total, total)
print(correct, correcPosWrongTC, wrongPos, total)
def multimapUTRRetainment (infile, outfile, bed, minIdentity, NM, log):
mappedReads = 0
unmappedReads = 0
filteredReads = 0
mqFiltered = 0
idFiltered = 0
nmFiltered = 0
utrIntervallTreeDict = bedToIntervallTree(bed)
# debugLog = os.path.join("multimapdebug.log")
#
# fo = open(debugLog, "w")
# Buffers for multimappers
multimapBuffer = {}
prevRead = ""
# If read maps to another than previously recorded UTR -> do not dump reads to file
dumpBuffer = True
# This string tracks all multiple alignments
multimapList = ""
# logList = []
for read in infile:
if(not read.is_secondary and not read.is_supplementary):
if(read.is_unmapped):
unmappedReads += 1
else:
mappedReads += 1
# First pass general filters
if(read.is_unmapped):
continue
if(float(read.get_tag("XI")) < minIdentity):
idFiltered += 1
continue
if(NM > -1 and int(read.get_tag("NM")) > NM):
nmFiltered += 1
continue
if (read.mapping_quality == 0) :
# Previous read was also multimapper
if (read.query_name != prevRead and prevRead != "") :
#if (dumpBuffer and (len(multimapBuffer) > 1 or len(multimapBuffer["nonUTR"]) > 0)) :
if (dumpBuffer and len(multimapBuffer) > 0) :
dumpBufferToBam(multimapBuffer, multimapList, outfile, infile)
filteredReads += 1
# ret = dumpBufferToBam(multimapBuffer, outfile, infile)
# print(ret,file = fo)
#multimapBuffer = {}
#multimapBuffer["nonUTR"] = []
# for entry in logList:
# print(prevRead + "\t" + entry + "\t" + str(dumpBuffer), file = fo)
# logList = []
dumpBuffer = True
multimapList = ""
multimapBuffer = {}
# Query Intervall tree for given chromosome for UTs
chr = infile.getrname(read.reference_id)
start = read.reference_start
end = read.reference_end
if (utrIntervallTreeDict.has_key(chr)) :
query = utrIntervallTreeDict[chr][start:end]
else :
query = set()
if len(query) > 0:
# First UTR hit is recorded without checks
if (len(multimapBuffer) == 0) :
for result in query :
if (not multimapBuffer.has_key(result.data)) :
multimapBuffer[result.data] = []
multimapBuffer[result.data].append(read)
# Second UTR hit looks at previous UTR hits -> no dump if hit on different UTR
else :
for result in query :
if (not multimapBuffer.has_key(result.data)) :
multimapBuffer[result.data] = []
multimapBuffer[result.data].append(read)
dumpBuffer = False
else :
multimapBuffer[result.data].append(read)
# else :
# # If no overlap -> nonUTR
# multimapBuffer["nonUTR"].append(read)
# for result in query :
# logList.append(chr + "\t" + str(start) + "\t" + str(end) + "\t" + result.data)
# else :
# logList.append(chr + "\t" + str(start) + "\t" + str(end) + "\t" + "OFF")
multimapList = multimapList + chr + ":" + str(start) + "-" + str(end) + " "
prevRead = read.query_name
else :
# Dump any multimappers before a unique mapper
#if (len(multimapBuffer) > 1 or len(multimapBuffer["nonUTR"]) > 0) :
if (len(multimapBuffer) > 0) :
if (dumpBuffer) :
dumpBufferToBam(multimapBuffer, multimapList, outfile, infile)
filteredReads += 1
# ret = dumpBufferToBam(multimapBuffer, outfile, infile)
# print(ret,file = fo)
multimapBuffer = {}
# for entry in logList:
# print(prevRead + "\t" + entry + "\t" + str(dumpBuffer), file = fo)
# logList = []
#multimapBuffer["nonUTR"] = []
dumpBuffer = True
multimapList = ""
# Record all unique mappers
prevRead = read.query_name
outfile.write(read)
filteredReads += 1
# Dump last portion if it was multimapper
#if (dumpBuffer and (len(multimapBuffer) > 1 or len(multimapBuffer["nonUTR"]) > 0)) :
if (dumpBuffer and len(multimapBuffer) > 0) :
dumpBufferToBam(multimapBuffer, multimapList, outfile, infile)
filteredReads += 1
multimapper = mappedReads - filteredReads - idFiltered - nmFiltered
print("Criterion\tFiltered reads",file=log)
print("MQ < 0\t0",file=log)
print("ID < " + str(minIdentity) + "\t" + str(idFiltered),file=log)
print("NM > " + str(NM) + "\t" + str(nmFiltered),file=log)
print("MM\t" + str(multimapper),file=log)
# fo.close()
return mappedReads, unmappedReads, filteredReads, mqFiltered, idFiltered, nmFiltered, multimapper
def multimapUTRRetainment(infile, outfile, bed, minIdentity, NM, log):
mappedReads = 0
unmappedReads = 0
filteredReads = 0
mqFiltered = 0
idFiltered = 0
nmFiltered = 0
utrIntervallTreeDict = bedToIntervallTree(bed)
# debugLog = os.path.join("multimapdebug.log")
#
# fo = open(debugLog, "w")
# Buffers for multimappers
multimapBuffer = {}
prevRead = ""
# If read maps to another than previously recorded UTR -> do not dump reads to file
dumpBuffer = True
# This string tracks all multiple alignments
multimapList = ""
# logList = []
for read in infile:
if (not read.is_secondary and not read.is_supplementary):
if (read.is_unmapped):
unmappedReads += 1
else:
mappedReads += 1
# First pass general filters
if (read.is_unmapped):
continue
if (float(read.get_tag("XI")) < minIdentity):
idFiltered += 1
continue
if (NM > -1 and int(read.get_tag("NM")) > NM):
nmFiltered += 1
continue
if (read.mapping_quality == 0):
# Previous read was also multimapper
if (read.query_name != prevRead and prevRead != ""):
#if (dumpBuffer and (len(multimapBuffer) > 1 or len(multimapBuffer["nonUTR"]) > 0)) :
if (dumpBuffer and len(multimapBuffer) > 0):
dumpBufferToBam(multimapBuffer, multimapList, outfile,
infile)
filteredReads += 1
# ret = dumpBufferToBam(multimapBuffer, outfile, infile)
# print(ret,file = fo)
#multimapBuffer = {}
#multimapBuffer["nonUTR"] = []
# for entry in logList:
# print(prevRead + "\t" + entry + "\t" + str(dumpBuffer), file = fo)
# logList = []
dumpBuffer = True
multimapList = ""
multimapBuffer = {}
# Query Intervall tree for given chromosome for UTs
chr = infile.getrname(read.reference_id)
start = read.reference_start
end = read.reference_end
if (chr in utrIntervallTreeDict):
query = utrIntervallTreeDict[chr][start:end]
else:
query = set()
if len(query) > 0:
# First UTR hit is recorded without checks
if (len(multimapBuffer) == 0):
for result in query:
if (not result.data in multimapBuffer):
multimapBuffer[result.data] = []
multimapBuffer[result.data].append(read)
# Second UTR hit looks at previous UTR hits -> no dump if hit on different UTR
else:
for result in query:
if (not result.data in multimapBuffer):
multimapBuffer[result.data] = []
multimapBuffer[result.data].append(read)
dumpBuffer = False
else:
multimapBuffer[result.data].append(read)
# else :
# # If no overlap -> nonUTR
# multimapBuffer["nonUTR"].append(read)
# for result in query :
# logList.append(chr + "\t" + str(start) + "\t" + str(end) + "\t" + result.data)
# else :
# logList.append(chr + "\t" + str(start) + "\t" + str(end) + "\t" + "OFF")
multimapList = multimapList + chr + ":" + str(start) + "-" + str(
end) + " "
prevRead = read.query_name
else:
# Dump any multimappers before a unique mapper
#if (len(multimapBuffer) > 1 or len(multimapBuffer["nonUTR"]) > 0) :
if (len(multimapBuffer) > 0):
if (dumpBuffer):
dumpBufferToBam(multimapBuffer, multimapList, outfile,
infile)
filteredReads += 1
# ret = dumpBufferToBam(multimapBuffer, outfile, infile)
# print(ret,file = fo)
multimapBuffer = {}
# for entry in logList:
# print(prevRead + "\t" + entry + "\t" + str(dumpBuffer), file = fo)
# logList = []
#multimapBuffer["nonUTR"] = []
dumpBuffer = True
multimapList = ""
# Record all unique mappers
prevRead = read.query_name
outfile.write(read)
filteredReads += 1
# Dump last portion if it was multimapper
#if (dumpBuffer and (len(multimapBuffer) > 1 or len(multimapBuffer["nonUTR"]) > 0)) :
if (dumpBuffer and len(multimapBuffer) > 0):
dumpBufferToBam(multimapBuffer, multimapList, outfile, infile)
filteredReads += 1
multimapper = mappedReads - filteredReads - idFiltered - nmFiltered
print("Criterion\tFiltered reads", file=log)
print("MQ < 0\t0", file=log)
print("ID < " + str(minIdentity) + "\t" + str(idFiltered), file=log)
print("NM > " + str(NM) + "\t" + str(nmFiltered), file=log)
print("MM\t" + str(multimapper), file=log)
# fo.close()
return mappedReads, unmappedReads, filteredReads, mqFiltered, idFiltered, nmFiltered, multimapper
def multimapUTRRetainment(infile, outfile, bed, minIdentity, NM, MQ, log):
mappedReads, unmappedReads, filteredReads, mqFiltered, idFiltered, nmFiltered = 0, 0, 0, 0, 0, 0
utrIntervallTreeDict = bedToIntervallTree(
bed) # Is interpreted now to represent any entity in the bed file
# Buffers for multimappers
multimapBuffer = {}
prevRead = ""
# If read maps to another than previously recorded UTR -> do not dump reads to file
dumpBuffer = True
# This string tracks all multiple alignments
multimapList = ""
for read in infile: # infile is AlignedFile according to pysam definition. Read is AlignedSegment
if not read.is_secondary and not read.is_supplementary:
if read.is_unmapped:
unmappedReads += 1
else:
mappedReads += 1
# First pass general filters
if read.is_unmapped:
continue
if float(read.get_tag("XI")) < minIdentity:
idFiltered += 1
continue
if -1 < NM < int(read.get_tag("NM")):
nmFiltered += 1
continue
if read.mapping_quality < MQ:
# Previous read was also multimapper
if read.query_name != prevRead and prevRead != "":
if dumpBuffer and len(multimapBuffer) > 0:
dumpBufferToBam(multimapBuffer, multimapList, outfile,
infile)
filteredReads += 1
dumpBuffer = True
multimapList = ""
multimapBuffer = {}
# Query Intervall tree for given chromosome for UTRs
chr = infile.get_reference_name(read.reference_id)
start = read.reference_start
end = read.reference_end
if chr in utrIntervallTreeDict:
query = utrIntervallTreeDict[chr][
start:
end] # This makes sure that mapping is in a bed region
else:
query = set()
if len(query) > 0:
# First UTR hit is recorded without checks
if len(multimapBuffer) == 0:
for result in query:
if result.data not in multimapBuffer:
multimapBuffer[result.data] = []
multimapBuffer[result.data].append(read)
# Second UTR hit looks at previous UTR hits -> no dump if hit on different UTR
else:
for result in query:
if result.data not in multimapBuffer:
multimapBuffer[result.data] = []
multimapBuffer[result.data].append(read)
dumpBuffer = False
else:
multimapBuffer[result.data].append(read)
multimapList = multimapList + chr + ":" + str(start) + "-" + str(
end) + " "
prevRead = read.query_name
else: # If read.mapping_quality > mq
# Dump any multimappers before a unique mapper
if len(multimapBuffer) > 0:
if dumpBuffer:
dumpBufferToBam(multimapBuffer, multimapList, outfile,
infile)
filteredReads += 1
multimapBuffer = {}
dumpBuffer = True
multimapList = ""
# Record all unique mappers
prevRead = read.query_name
outfile.write(read)
filteredReads += 1
# Dump last portion if it was multimapper
if dumpBuffer and len(multimapBuffer) > 0:
dumpBufferToBam(multimapBuffer, multimapList, outfile, infile)
filteredReads += 1
multimapper = mappedReads - filteredReads - idFiltered - nmFiltered
print("Criterion\tFiltered reads", file=log)
print("MQ < 0\t0", file=log)
print("ID < %s\t%s" % (minIdentity, idFiltered), file=log)
print("NM > %s\t%s" % (NM, nmFiltered), file=log)
print("MM\t%s" % multimapper, file=log)
return mappedReads, unmappedReads, filteredReads, mqFiltered, idFiltered, nmFiltered, multimapper