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 __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)
@classmethod
def extractOneTrackManyRegsToOneFile(cls, trackName, regionList, fn, fileFormatName=DEFAULT_FILE_FORMAT_NAME, \
globalCoords=False, asOriginal=False, allowOverlaps=False):
cls.extract(trackName, regionList, fn, fileFormatName=fileFormatName, globalCoords=globalCoords, \
addSuffix=False, asOriginal=asOriginal, allowOverlaps=allowOverlaps)
@classmethod
def extractManyToOneDir(cls, trackNameList, regionList, baseDir, fileFormatName=DEFAULT_FILE_FORMAT_NAME, \
globalCoords=False, asOriginal=False, allowOverlaps=False):
for trackName in trackNameList:
fn = baseDir + os.sep + '_'.join(trackName)
cls.extractOneTrackManyRegsToOneFile(trackName, regionList, fn, fileFormatName=fileFormatName,
globalCoords=globalCoords, asOriginal=asOriginal, \
allowOverlaps=allowOverlaps)
if __name__ == "__main__":
if len(sys.argv) not in [4, 5]:
print 'Syntax: python TrackExtractor.py trackName:subtype genome:chr:start-end asOriginal [filename]'
sys.exit(0)
trackName = parseTrackNameSpec(sys.argv[1])
regions = parseRegSpec(sys.argv[2])
assert len(regions) == 1
asOriginal = eval(sys.argv[3])
fn = sys.argv[4] if len(sys.argv) == 5 else None
TrackExtractor.extract(trackName, regions[0], fn, asOriginal=asOriginal)
zipFile.close()
@classmethod
def extractOneTrackManyRegsToOneFile(cls, trackName, regionList, fn, fileFormatName=DEFAULT_FILE_FORMAT_NAME, \
globalCoords=False, asOriginal=False, allowOverlaps=False):
cls.extract(trackName, regionList, fn, fileFormatName=fileFormatName, globalCoords=globalCoords, \
addSuffix=False, asOriginal=asOriginal, allowOverlaps=allowOverlaps)
@classmethod
def extractManyToOneDir(cls, trackNameList, regionList, baseDir, fileFormatName=DEFAULT_FILE_FORMAT_NAME, \
globalCoords=False, asOriginal=False, allowOverlaps=False):
for trackName in trackNameList:
fn = baseDir + os.sep + '_'.join(trackName)
cls.extractOneTrackManyRegsToOneFile(trackName, regionList, fn, fileFormatName=fileFormatName,
globalCoords=globalCoords, asOriginal=asOriginal, \
allowOverlaps=allowOverlaps)
if __name__ == "__main__":
if len(sys.argv) not in [4, 5]:
print 'Syntax: python TrackExtractor.py trackName:subtype genome:chr:start-end asOriginal [filename]'
sys.exit(0)
trackName = parseTrackNameSpec(sys.argv[1])
regions = parseRegSpec(sys.argv[2])
assert len(regions) == 1
asOriginal = eval(sys.argv[3])
fn = sys.argv[4] if len(sys.argv) == 5 else None
TrackExtractor.extract(trackName, regions[0], fn, asOriginal=asOriginal)