strandfilter=None, combine5p=False):
shiftValue = determineShiftValue(autoshift, shift, noshift, rnaSettings)
strandfilter=None, combine5p=False):
shiftValue = determineShiftValue(autoshift, shift, noshift, rnaSettings)
-
- if trimValue is not None:
- trimValue = float(trimValue) / 100.
- trimString = "%2.1f%s" % ((100. * trimValue), "%")
- else:
- trimValue = 0.1
- trimString = "10%"
-
- if not doTrim:
- trimString = "none"
+ doControl = False
+ if mockfile is not None:
+ doControl = True
stringency = max(stringency, 1.0)
writeLog(logfilename, versionString, string.join(sys.argv[1:]))
stringency = max(stringency, 1.0)
writeLog(logfilename, versionString, string.join(sys.argv[1:]))
foldRatio = getFoldRatio(mockRDS, chrom, regionStart, regionStop, doControl, useMulti, normalize, mockSampleSize, sumAll, minRatio)
if foldRatio >= minRatio:
foldRatio = getFoldRatio(mockRDS, chrom, regionStart, regionStop, doControl, useMulti, normalize, mockSampleSize, sumAll, minRatio)
if foldRatio >= minRatio:
- localshift = getBestShiftForRegion(readList, regionStart, regionLength, doWeight=True)
+ localshift = getBestShiftForRegion(readList, regionStart, regionLength, useWeight=True)
def locateRegions(rds, rdsSampleSize, referenceRDS, referenceSampleSize, chrom, useMulti,
def locateRegions(rds, rdsSampleSize, referenceRDS, referenceSampleSize, chrom, useMulti,
- normalize, maxSpacing, doDirectionality, doTrim, minHits, minRatio, readlen,
+ normalizeToRPM, maxSpacing, doDirectionality, doTrim, minHits, minRatio, readlen,
shiftValue, minPeak, minPlusRatio, maxPlusRatio, leftPlusRatio, listPeak,
noMulti, doControl, factor, trimValue, outputRegionList=False):
shiftValue, minPeak, minPlusRatio, maxPlusRatio, leftPlusRatio, listPeak,
noMulti, doControl, factor, trimValue, outputRegionList=False):
if sumAll >= minHits and numStarts > minRatio and (regionStop - regionStart) > readlen:
sumMulti = 0.
#first pass uses getFoldRatio on mockRDS as there may not be control
if sumAll >= minHits and numStarts > minRatio and (regionStop - regionStart) > readlen:
sumMulti = 0.
#first pass uses getFoldRatio on mockRDS as there may not be control
- foldRatio = getFoldRatioFromRDS(referenceRDS, chrom, regionStart, regionStop, useMulti, normalize, referenceSampleSize, sumAll)
+ foldRatio = getFoldRatioFromRDS(referenceRDS, chrom, regionStart, regionStop, useMulti, normalizeToRPM, referenceSampleSize, sumAll)
if foldRatio >= minRatio:
# first pass, with absolute numbers
peak = findPeak(currentReadList, regionStart, regionStop - regionStart, readlen, doWeight=True, leftPlus=doDirectionality, shift=shiftValue)
if foldRatio >= minRatio:
# first pass, with absolute numbers
peak = findPeak(currentReadList, regionStart, regionStop - regionStart, readlen, doWeight=True, leftPlus=doDirectionality, shift=shiftValue)
- foldRatio = getFoldRatio(referenceRDS, chrom, regionStart, regionStop, doControl, useMulti, normalize, referenceSampleSize, sumAll, minRatio)
+ foldRatio = getFoldRatio(referenceRDS, chrom, regionStart, regionStop, doControl, useMulti, normalizeToRPM, referenceSampleSize, sumAll, minRatio)
if outputRegionList:
sumMulti = rds.getCounts(chrom, regionStart, regionStop, uniqs=False, multi=useMulti, splices=False, reportCombined=True)
# just in case it changed, use latest data
if outputRegionList:
sumMulti = rds.getCounts(chrom, regionStart, regionStop, uniqs=False, multi=useMulti, splices=False, reportCombined=True)
# just in case it changed, use latest data