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 getGESource(fullFn,
fileSuffix,
extTrackName=None,
genome=None,
printWarnings=False):
from gtrackcore.input.core.GenomeElementSource import GenomeElementSource
return GenomeElementSource(fullFn,
suffix=fileSuffix,
forPreProcessor=True,
genome=genome,
trackName=extTrackName,
external=True,
printWarnings=printWarnings)
def _allGESources(self, trackName):
baseDir = createOrigPath(self._genome, trackName)
self._status = 'Trying os.listdir on: ' + baseDir
for relFn in sorted(os.listdir(baseDir)):
fn = os.sep.join([baseDir, relFn])
self._status = 'Checking file: ' + fn
if os.path.isdir(fn):
continue
fnPart = os.path.split(fn)[-1]
if fnPart[0] in ['.', '_', '#'] or fnPart[-1] in [
'~', '#'
]: #to avoid hidden files..
continue
self._status = 'Trying to create geSource from fn: ' + fn
yield GenomeElementSource(fn, self._genome, forPreProcessor=True)
def _commonStandardizeGtrackFile(fn, genome, suffix=None):
geSource = GenomeElementSource(fn, genome, suffix=suffix)
composedFile = StdGtrackComposer(
GtrackElementStandardizer(geSource)).returnComposed()
return expandHeadersOfGtrackFileAndReturnComposer(
'', genome, strToUseInsteadOfFn=composedFile)
