def _commonExportFile(outFileName, genome, trackName, fileFormatName, allowOverlaps, bins):
trackName = _convertTrackName(trackName)
if not _trackNameExists(genome, trackName):
return
outFileName = os.path.abspath(outFileName)
from gtrackcore_memmap.extract.TrackExtractor import TrackExtractor
TrackExtractor.extractOneTrackManyRegsToOneFile(
trackName,
bins,
outFileName,
fileFormatName=fileFormatName,
globalCoords=True,
asOriginal=False,
allowOverlaps=allowOverlaps,
)
def getExtractionOptions(genome, trackName):
"""genome trackName"""
trackName = _convertTrackName(trackName)
if not _trackNameExists(genome, trackName):
return
print
print 'Available extraction options for track "%s" of genome "%s":' % (":".join(trackName), genome)
print
print "{:<19}".format("fileFormatName") + "{:<17}".format("allowOverlaps") + "Description"
print "-" * 80
from gtrackcore_memmap.extract.TrackExtractor import TrackExtractor
for text, suffix in TrackExtractor.getTrackExtractionOptions(genome, trackName):
fileFormatName, asOriginal, allowOverlaps = TrackExtractor.getAttrsFromExtractionFormat(text)
print "{:<19}".format(fileFormatName) + "{:<17}".format(str(allowOverlaps)) + text
