import ReadDataset
INSERT_SIZE = 100000
-verstring = "makeRdsFromBam: version 1.0"
+verstring = "makeRdsFromBam: version 1.1"
def main(argv=None):
print "no outrdsfile specified - see --help for usage"
sys.exit(1)
+ if options.rnaDataType:
+ dataType = "RNA"
+ else:
+ dataType = "DNA"
+
makeRdsFromBam(label, samFileName, outDbName, options.init, options.doIndex, options.useSamFile,
- options.cachePages, options.maxMultiReadCount, options.rnaDataType, options.trimReadID)
+ options.cachePages, options.maxMultiReadCount, dataType, options.trimReadID)
def getParser(usage):
def makeRdsFromBam(label, samFileName, outDbName, init=True, doIndex=False, useSamFile=False,
- cachePages=100000, maxMultiReadCount=10, rnaDataType=False, trimReadID=True):
+ cachePages=100000, maxMultiReadCount=10, dataType="DNA", trimReadID=True):
if useSamFile:
fileMode = "r"
else:
fileMode = "rb"
- try:
- samfile = pysam.Samfile(samFileName, fileMode)
- except ValueError:
- print "samfile index not found"
- sys.exit(1)
-
- if rnaDataType:
- dataType = "RNA"
- else:
- dataType = "DNA"
-
writeLog("%s.log" % outDbName, verstring, string.join(sys.argv[1:]))
-
rds = ReadDataset.ReadDataset(outDbName, init, dataType, verbose=True)
if not init and doIndex:
try:
"unique": 0,
"multi": 0,
"multiDiscard": 0,
- "splice": 0
+ "splice": 0,
+ "multisplice": 0
}
readsize = 0
uniqueInsertList = []
multiInsertList = []
spliceInsertList = []
+ multispliceInsertList = []
- processedEntryDict = {}
uniqueReadDict = {}
multiReadDict = {}
+ multispliceReadDict = {}
spliceReadDict = {}
+ multireadCounts = getMultiReadIDCounts(samFileName, fileMode)
- samFileIterator = samfile.fetch(until_eof=True)
+ for readID in multireadCounts:
+ if multireadCounts[readID] > maxMultiReadCount:
+ totalReadCounts["multiDiscard"] += 1
+
+ try:
+ samfile = pysam.Samfile(samFileName, fileMode)
+ except ValueError:
+ print "samfile index not found"
+ sys.exit(1)
+ samFileIterator = samfile.fetch(until_eof=True)
for read in samFileIterator:
if read.is_unmapped:
totalReadCounts["unmapped"] += 1
if init:
rds.insertMetadata([("readsize", readsize)])
- #Build the read dictionaries
- try:
- readSequence = read.seq
- except KeyError:
- readSequence = ""
-
pairReadSuffix = getPairedReadNumberSuffix(read)
- readName = "%s%s%s" % (read.qname, readSequence, pairReadSuffix)
+ readName = "%s%s" % (read.qname, pairReadSuffix)
if trimReadID:
rdsEntryName = "%s:%s:%d%s" % (label, read.qname, totalReadCounts["total"], pairReadSuffix)
else:
rdsEntryName = read.qname
- if processedEntryDict.has_key(readName):
- if isSpliceEntry(read.cigar):
- if spliceReadDict.has_key(readName):
- del spliceReadDict[readName]
- else:
- if uniqueReadDict.has_key(readName):
- del uniqueReadDict[readName]
-
- if multiReadDict.has_key(readName):
- (read, priorCount, rdsEntryName) = multiReadDict[readName]
- count = priorCount + 1
- multiReadDict[readName] = (read, count, rdsEntryName)
- else:
- multiReadDict[readName] = (read, 1, rdsEntryName)
- else:
- processedEntryDict[readName] = ""
+ try:
+ count = multireadCounts[readName]
+ except KeyError:
+ count = 1
+
+ if count == 1:
if isSpliceEntry(read.cigar):
spliceReadDict[readName] = (read,rdsEntryName)
else:
uniqueReadDict[readName] = (read, rdsEntryName)
+ elif count <= maxMultiReadCount:
+ if isSpliceEntry(read.cigar):
+ multispliceReadDict[readName] = (read, count, rdsEntryName)
+ else:
+ multiReadDict[readName] = (read, count, rdsEntryName)
if totalReadCounts["total"] % INSERT_SIZE == 0:
for entry in uniqueReadDict.keys():
uniqueInsertList.append(getRDSEntry(readData, rdsEntryName, chrom, readsize))
totalReadCounts["unique"] += 1
- for entry in spliceReadDict.keys():
- (readData, rdsEntryName) = spliceReadDict[entry]
- chrom = samfile.getrname(readData.rname)
- spliceInsertList.append(getRDSSpliceEntry(readData, rdsEntryName, chrom, readsize))
- totalReadCounts["splice"] += 1
-
for entry in multiReadDict.keys():
(readData, count, rdsEntryName) = multiReadDict[entry]
chrom = samfile.getrname(readData.rname)
- if count > maxMultiReadCount:
- totalReadCounts["multiDiscard"] += 1
- else:
- multiInsertList.append(getRDSEntry(readData, rdsEntryName, chrom, readsize, weight=count))
- totalReadCounts["multi"] += 1
+ multiInsertList.append(getRDSEntry(readData, rdsEntryName, chrom, readsize, weight=count))
+
+ if dataType == "RNA":
+ for entry in spliceReadDict.keys():
+ (readData, rdsEntryName) = spliceReadDict[entry]
+ chrom = samfile.getrname(readData.rname)
+ spliceInsertList.append(getRDSSpliceEntry(readData, rdsEntryName, chrom, readsize))
+ totalReadCounts["splice"] += 1
+
+ for entry in multispliceReadDict.keys():
+ (readData, count, rdsEntryName) = multispliceReadDict[entry]
+ chrom = samfile.getrname(readData.rname)
+ multispliceInsertList.append(getRDSSpliceEntry(readData, rdsEntryName, chrom, readsize, weight=count))
+ totalReadCounts["multisplice"] += 1
rds.insertUniqs(uniqueInsertList)
rds.insertMulti(multiInsertList)
rds.insertSplices(spliceInsertList)
spliceInsertList = []
spliceReadDict = {}
+ rds.insertMultisplices(multispliceInsertList)
+ multispliceInsertList = []
+ multispliceReadDict = {}
print ".",
sys.stdout.flush()
- processedEntryDict = {}
totalReadCounts["total"] += 1
for entry in multiReadDict.keys():
(readData, count, rdsEntryName) = multiReadDict[entry]
chrom = samfile.getrname(readData.rname)
- if count > maxMultiReadCount:
- totalReadCounts["multiDiscard"] += 1
- else:
- multiInsertList.append(getRDSEntry(readData, rdsEntryName, chrom, readsize, weight=count))
- totalReadCounts["multi"] += 1
+ multiInsertList.append(getRDSEntry(readData, rdsEntryName, chrom, readsize, weight=count))
- totalReadCounts["multi"] += len(multiInsertList)
+ rds.insertMulti(multiInsertList)
if len(spliceReadDict.keys()) > 0 and dataType == "RNA":
for entry in spliceReadDict.keys():
rds.insertSplices(spliceInsertList)
+ if len(multispliceReadDict.keys()) > 0 and dataType == "RNA":
+ for entry in multispliceReadDict.keys():
+ (readData, count, rdsEntryName) = multispliceReadDict[entry]
+ chrom = samfile.getrname(readData.rname)
+ multispliceInsertList.append(getRDSSpliceEntry(readData, rdsEntryName, chrom, readsize, weight=count))
+ totalReadCounts["multisplice"] += 1
+
+ rds.insertMultisplices(multispliceInsertList)
+
+ totalReadCounts["multi"] = len(multireadCounts) - totalReadCounts["multiDiscard"] - totalReadCounts["multisplice"]
countStringList = ["\n%d unmapped reads discarded" % totalReadCounts["unmapped"]]
countStringList.append("%d unique reads" % totalReadCounts["unique"])
countStringList.append("%d multi reads" % totalReadCounts["multi"])
countStringList.append("%d multi reads count > %d discarded" % (totalReadCounts["multiDiscard"], maxMultiReadCount))
if dataType == "RNA":
countStringList.append("%d spliced reads" % totalReadCounts["splice"])
+ countStringList.append("%d spliced multireads" % totalReadCounts["multisplice"])
print string.join(countStringList, "\n")
outputCountText = string.join(countStringList, "\t")
rds.buildIndex(defaultCacheSize)
+def getMultiReadIDCounts(samFileName, fileMode):
+ try:
+ samfile = pysam.Samfile(samFileName, fileMode)
+ except ValueError:
+ print "samfile index not found"
+ sys.exit(1)
+
+ readIDCounts = {}
+ for read in samfile.fetch(until_eof=True):
+ pairReadSuffix = getPairedReadNumberSuffix(read)
+ readName = "%s%s" % (read.qname, pairReadSuffix)
+ try:
+ readIDCounts[readName] += 1
+ except KeyError:
+ readIDCounts[readName] = 1
+
+ for readID in readIDCounts.keys():
+ if readIDCounts[readID] == 1:
+ del readIDCounts[readID]
+
+ return readIDCounts
+
+
def getRDSEntry(alignedRead, readName, chrom, readSize, weight=1):
start = int(alignedRead.pos)
stop = int(start + readSize)
return (readName, chrom, start, stop, sense, 1.0/weight, '', mismatches)
-def getRDSSpliceEntry(alignedRead, readName, chrom, readSize):
- (readName, chrom, start, stop, sense, weight, flag, mismatches) = getRDSEntry(alignedRead, readName, chrom, readSize)
+def getRDSSpliceEntry(alignedRead, readName, chrom, readSize, weight=1):
+ (readName, chrom, start, stop, sense, weight, flag, mismatches) = getRDSEntry(alignedRead, readName, chrom, readSize, weight)
startL, startR, stopL, stopR = getSpliceBounds(start, readSize, alignedRead.cigar)
- return (readName, chrom, startL, stopL, startR, stopR, sense, 1.0, "", mismatches)
+ return (readName, chrom, startL, stopL, startR, stopR, sense, weight, "", mismatches)
def getPairedReadNumberSuffix(read):
projects / erange.git / blobdiff