def __new__(cls, regSpec, binSpec, genome=None, categoryFilterList=None, strictMatch=True, includeExtraChrs = False): #,fileType): if regSpec in ['file', 'track'] + getSupportedFileSuffixesForBinning(): #if fileType != 'bed': # raise NotImplementedError assert genome is not None from gtrackcore_memmap.input.core.GenomeElementSource import GenomeElementSource if regSpec == 'file': geSource = GenomeElementSource(binSpec, genome=genome) elif regSpec == 'track': from gtrackcore_memmap.input.adapters.TrackGenomeElementSource import FullTrackGenomeElementSource trackName = convertTNstrToTNListFormat(binSpec) geSource = FullTrackGenomeElementSource(genome, trackName, allowOverlaps=False) else: geSource = GenomeElementSource(binSpec, genome=genome, suffix=regSpec) if categoryFilterList is not None: from gtrackcore_memmap.input.wrappers.GECategoryFilter import GECategoryFilter geSource = GECategoryFilter(geSource, categoryFilterList, strict=strictMatch) return cls._applyEnvelope(geSource) else: if binSpec == '*': binSize = None else: binSize = parseShortenedSizeSpec(binSpec) from gtrackcore_memmap.input.userbins.AutoBinner import AutoBinner return AutoBinner(parseRegSpec(regSpec, genome, includeExtraChrs=includeExtraChrs), binSize)
def __init__(self, origTrack, origRegion, randIndex, trackNameIntensity="", **kwArgs): #print 'INTENSITY TRACK IS USED: ',trackNameIntensity self._minimal = ('minimal' in kwArgs and kwArgs['minimal'] == True) #from gtrackcore_memmap.util.CommonFunctions import isIter #from gtrackcore_memmap.util.CustomExceptions import SplittableStatNotAvailableError #if isIter(origRegion): # raise SplittableStatNotAvailableError RandomizedTrack.__init__(self, origTrack, origRegion, randIndex, trackNameIntensity=trackNameIntensity, **kwArgs) #self._trackNameIntensity = [unquote(x) for x in convertTNstrToTNListFormat(trackNameIntensity)] self._trackNameIntensity = convertTNstrToTNListFormat(trackNameIntensity)
def _convertTrackName(trackName): from gtrackcore_memmap.util.CommonFunctions import convertTNstrToTNListFormat return convertTNstrToTNListFormat(trackName, doUnquoting=True)