except:
pass
-import sys, string, optparse, re
+import sys
+import string
+import optparse
+import re
import pysam
-from commoncode import readDataset, writeLog
+from commoncode import writeLog, getConfigParser, getConfigBoolOption, getConfigIntOption, getReverseComplement
+import ReadDataset
-verstring = "%prog: version 1.0"
+INSERT_SIZE = 100000
+verstring = "makeRdsFromBam: version 1.0"
def main(argv=None):
usage = "usage: %prog label samfile outrdsfile [propertyName::propertyValue] [options]\
\ninput reads must be sorted to properly record multireads"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--append", action="store_false", dest="init",
- help="append to existing rds file [default: create new]")
- parser.add_option("--RNA", action="store_true", dest="rnaDataType",
- help="set data type to RNA [default: DNA]")
- parser.add_option("-S", "--sam", action="store_true", dest="useSamFile",
- help="input file is in sam format")
- parser.add_option("--index", action="store_true", dest="doIndex",
- help="index the output rds file")
- parser.add_option("--cache", type="int", dest="cachePages",
- help="number of cache pages to use [default: 100000")
- parser.add_option("-m", "--multiCount", type="int", dest="maxMultiReadCount",
- help="multi counts over this value are discarded [default: 10]")
- parser.add_option("--rawreadID", action="store_false", dest="trimReadID",
- help="use the raw read names")
- parser.set_defaults(init=True, doIndex=False, useSamFile=False, cachePages=100000,
- maxMultiReadCount=10, rnaDataType=False, trimReadID=True)
-
+ parser = getParser(usage)
(options, args) = parser.parse_args(argv[1:])
try:
options.cachePages, options.maxMultiReadCount, options.rnaDataType, options.trimReadID)
+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--append", action="store_false", dest="init",
+ help="append to existing rds file [default: create new]")
+ parser.add_option("--RNA", action="store_true", dest="rnaDataType",
+ help="set data type to RNA [default: DNA]")
+ parser.add_option("-S", "--sam", action="store_true", dest="useSamFile",
+ help="input file is in sam format")
+ parser.add_option("--index", action="store_true", dest="doIndex",
+ help="index the output rds file")
+ parser.add_option("--cache", type="int", dest="cachePages",
+ help="number of cache pages to use [default: 100000")
+ parser.add_option("-m", "--multiCount", type="int", dest="maxMultiReadCount",
+ help="multi counts over this value are discarded [default: 10]")
+ parser.add_option("--rawreadID", action="store_false", dest="trimReadID",
+ help="use the raw read names")
+
+ configParser = getConfigParser()
+ section = "makeRdsFromBam"
+ init = getConfigBoolOption(configParser, section, "init", True)
+ doIndex = getConfigBoolOption(configParser, section, "doIndex", False)
+ useSamFile = getConfigBoolOption(configParser, section, "useSamFile", False)
+ cachePages = getConfigIntOption(configParser, section, "cachePages", 100000)
+ maxMultiReadCount = getConfigIntOption(configParser, section, "maxMultiReadCount", 10)
+ rnaDataType = getConfigBoolOption(configParser, section, "rnaDataType", False)
+ trimReadID = getConfigBoolOption(configParser, section, "trimReadID", True)
+
+ parser.set_defaults(init=init, doIndex=doIndex, useSamFile=useSamFile, cachePages=cachePages,
+ maxMultiReadCount=maxMultiReadCount, rnaDataType=rnaDataType, trimReadID=trimReadID)
+
+ return parser
+
+
def makeRdsFromBam(label, samFileName, outDbName, init=True, doIndex=False, useSamFile=False,
cachePages=100000, maxMultiReadCount=10, rnaDataType=False, trimReadID=True):
writeLog("%s.log" % outDbName, verstring, string.join(sys.argv[1:]))
- rds = readDataset(outDbName, init, dataType, verbose=True)
+ rds = ReadDataset.ReadDataset(outDbName, init, dataType, verbose=True)
if not init and doIndex:
try:
if rds.hasIndex():
if len(propertyList) > 0:
rds.insertMetadata(propertyList)
- countReads = {"unmapped": 0,
- "total": 0,
- "unique": 0,
- "multi": 0,
- "multiDiscard": 0,
- "splice": 0
+ totalReadCounts = {"unmapped": 0,
+ "total": 0,
+ "unique": 0,
+ "multi": 0,
+ "multiDiscard": 0,
+ "splice": 0
}
readsize = 0
- insertSize = 100000
uniqueInsertList = []
multiInsertList = []
for read in samFileIterator:
if read.is_unmapped:
- countReads["unmapped"] += 1
+ totalReadCounts["unmapped"] += 1
continue
if readsize == 0:
- take = (0, 2, 3) # CIGAR operation (M/match, D/del, N/ref_skip)
+ take = (0, 1) # CIGAR operation (M/match, I/insertion)
readsize = sum([length for op,length in read.cigar if op in take])
if init:
rds.insertMetadata([("readsize", readsize)])
pairReadSuffix = getPairedReadNumberSuffix(read)
readName = "%s%s%s" % (read.qname, readSequence, pairReadSuffix)
if trimReadID:
- rdsEntryName = "%s:%s:%d%s" % (label, read.qname, countReads["total"], pairReadSuffix)
+ rdsEntryName = "%s:%s:%d%s" % (label, read.qname, totalReadCounts["total"], pairReadSuffix)
else:
rdsEntryName = read.qname
else:
uniqueReadDict[readName] = (read, rdsEntryName)
- if countReads["total"] % insertSize == 0:
+ if totalReadCounts["total"] % INSERT_SIZE == 0:
for entry in uniqueReadDict.keys():
(readData, rdsEntryName) = uniqueReadDict[entry]
chrom = samfile.getrname(readData.rname)
uniqueInsertList.append(getRDSEntry(readData, rdsEntryName, chrom, readsize))
- countReads["unique"] += 1
+ totalReadCounts["unique"] += 1
for entry in spliceReadDict.keys():
(readData, rdsEntryName) = spliceReadDict[entry]
chrom = samfile.getrname(readData.rname)
spliceInsertList.append(getRDSSpliceEntry(readData, rdsEntryName, chrom, readsize))
- countReads["splice"] += 1
+ totalReadCounts["splice"] += 1
for entry in multiReadDict.keys():
(readData, count, rdsEntryName) = multiReadDict[entry]
chrom = samfile.getrname(readData.rname)
if count > maxMultiReadCount:
- countReads["multiDiscard"] += 1
+ totalReadCounts["multiDiscard"] += 1
else:
multiInsertList.append(getRDSEntry(readData, rdsEntryName, chrom, readsize, weight=count))
- countReads["multi"] += 1
+ totalReadCounts["multi"] += 1
rds.insertUniqs(uniqueInsertList)
rds.insertMulti(multiInsertList)
sys.stdout.flush()
processedEntryDict = {}
- countReads["total"] += 1
+ totalReadCounts["total"] += 1
if len(uniqueReadDict.keys()) > 0:
for entry in uniqueReadDict.keys():
(readData, rdsEntryName) = uniqueReadDict[entry]
chrom = samfile.getrname(readData.rname)
uniqueInsertList.append(getRDSEntry(readData, rdsEntryName, chrom, readsize))
- countReads["unique"] += 1
+ totalReadCounts["unique"] += 1
rds.insertUniqs(uniqueInsertList)
(readData, count, rdsEntryName) = multiReadDict[entry]
chrom = samfile.getrname(readData.rname)
if count > maxMultiReadCount:
- countReads["multiDiscard"] += 1
+ totalReadCounts["multiDiscard"] += 1
else:
multiInsertList.append(getRDSEntry(readData, rdsEntryName, chrom, readsize, weight=count))
- countReads["multi"] += 1
+ totalReadCounts["multi"] += 1
- countReads["multi"] += len(multiInsertList)
+ totalReadCounts["multi"] += len(multiInsertList)
if len(spliceReadDict.keys()) > 0 and dataType == "RNA":
for entry in spliceReadDict.keys():
(readData, rdsEntryName) = spliceReadDict[entry]
chrom = samfile.getrname(readData.rname)
spliceInsertList.append(getRDSSpliceEntry(readData, rdsEntryName, chrom, readsize))
- countReads["splice"] += 1
+ totalReadCounts["splice"] += 1
rds.insertSplices(spliceInsertList)
- countString = "\n%d unmapped reads discarded" % countReads["unmapped"]
- countString += "\t%d unique reads" % countReads["unique"]
- countString += "\t%d multi reads" % countReads["multi"]
- countString += "\t%d multi reads count > %d discarded" % (countReads["multiDiscard"], maxMultiReadCount)
+ 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":
- countString += "\t%d spliced reads" % countReads["splice"]
+ countStringList.append("%d spliced reads" % totalReadCounts["splice"])
- print countString.replace("\t", "\n")
-
- writeLog("%s.log" % outDbName, verstring, countString)
+ print string.join(countStringList, "\n")
+ outputCountText = string.join(countStringList, "\t")
+ writeLog("%s.log" % outDbName, verstring, outputCountText)
if doIndex:
print "building index...."
def getRDSEntry(alignedRead, readName, chrom, readSize, weight=1):
start = int(alignedRead.pos)
- stop = int(start+readSize)
+ stop = int(start + readSize)
sense = getReadSense(alignedRead.is_reverse)
try:
mismatchTag = alignedRead.opt("MD")
genomicNucleotide = "N"
if sense == "-":
- mismatch = getComplementNucleotide(mismatch)
- genomicNucleotide = getComplementNucleotide(genomicNucleotide)
+ mismatch = getReverseComplement(mismatch)
+ genomicNucleotide = getReverseComplement(genomicNucleotide)
- elandCompatiblePosition = int(position + 1)
- output.append("%s%d%s" % (mismatch, elandCompatiblePosition, genomicNucleotide))
+ erange1BasedElandCompatiblePosition = int(position + 1)
+ output.append("%s%d%s" % (mismatch, erange1BasedElandCompatiblePosition, genomicNucleotide))
position += 1
except IndexError:
if logErrors:
return string.join(output, ",")
-def getComplementNucleotide(nucleotide):
- complement = {"A": "T",
- "T": "A",
- "C": "G",
- "G": "C",
- "N": "N"
- }
-
- return complement[nucleotide]
-
-
def getSpliceBounds(start, readsize, cigarTupleList):
stopR = int(start + readsize)
offset = 0
projects / erange.git / blobdiff