def path(self):
from quick.application.ExternalTrackManager import ExternalTrackManager
pathParts = self._parsedUri.path.split('/')
if len(pathParts) == 2:
return ExternalTrackManager.getGalaxyFnFromEncodedDatasetId(
pathParts[1])
elif len(pathParts) > 2:
dir_ = ExternalTrackManager.getGalaxyFilesFnFromEncodedDatasetId(
pathParts[1])
return os.path.sep.join([dir_] + pathParts[2:])
return None
def __new__(cls,
regSpec,
binSpec,
genome=None,
categoryFilterList=None,
strictMatch=True):
if regSpec in ['file', 'track'] + getSupportedFileSuffixesForBinning():
if genome is None:
genome = DEFAULT_GENOME
from gold.origdata.GenomeElementSource import GenomeElementSource
if regSpec == 'track':
from quick.util.CommonFunctions import convertTNstrToTNListFormat
from gold.origdata.TrackGenomeElementSource import FullTrackGenomeElementSource
trackName = convertTNstrToTNListFormat(binSpec)
geSource = FullTrackGenomeElementSource(genome,
trackName,
allowOverlaps=False)
else:
from quick.application.ExternalTrackManager import ExternalTrackManager
try:
fn = ExternalTrackManager.getGalaxyFnFromEncodedDatasetId(
binSpec)
except:
fn = binSpec
geSource = GenomeElementSource(
fn,
genome=genome,
suffix=regSpec if regSpec != 'file' else None)
if categoryFilterList is not None:
from gold.origdata.GECategoryFilter import GECategoryFilter
geSource = GECategoryFilter(geSource,
categoryFilterList,
strict=strictMatch)
return cls._applyEnvelope(geSource)
else:
if binSpec == '*':
binSize = None
else:
binSize = parseShortenedSizeSpec(binSpec)
from quick.application.AutoBinner import AutoBinner
return AutoBinner(parseRegSpec(regSpec, genome), binSize)
