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.input.core.GenomeElementSource import GenomeElementSource
if regSpec == 'file':
geSource = GenomeElementSource(binSpec, genome=genome)
elif regSpec == 'track':
from gtrackcore.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.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.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.util.CommonFunctions import isIter
#from gtrackcore.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 __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.input.core.GenomeElementSource import GenomeElementSource
if regSpec == 'file':
geSource = GenomeElementSource(binSpec, genome=genome)
elif regSpec == 'track':
from gtrackcore.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.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.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.util.CommonFunctions import isIter
#from gtrackcore.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.util.CommonFunctions import convertTNstrToTNListFormat
return convertTNstrToTNListFormat(trackName, doUnquoting=True)
def _convertTrackName(trackName):
from gtrackcore.util.CommonFunctions import convertTNstrToTNListFormat
return convertTNstrToTNListFormat(trackName, doUnquoting=True)