def createTrackContentFromFile(genome, path, allowOverlaps):
# TODO fix
# trackName = trackName.split(':')
# NOT SYSTEM safe!! Fix this later!
trackName = path.split("/")[-1]
trackName = trackName.split(".")[0]
importTrackIntoGTrack(trackName, genome, path)
track = Track(trackName.split(":"))
# We do not want to set this..
track.addFormatReq(TrackFormatReq(allowOverlaps=False, borderHandling="crop"))
trackViewList = OrderedDict()
for region in genome.regions:
try:
trackViewList[region] = track.getTrackView(region)
except OSError:
# There can be regions that the track does not cover..
# This is a temp fix.. should be bare of the api
pass
return TrackContents(genome, trackViewList)
def _createTrackContent(self, trackName, allowOverlaps):
trackName = trackName.split(':')
track = Track(trackName)
track.addFormatReq(TrackFormatReq(allowOverlaps=allowOverlaps,
borderHandling='crop'))
trackViewList = OrderedDict()
print self.hg18
print(type(self.hg18))
for region in self.hg18:
print(region)
print(type(region))
trackViewList[region] = track.getTrackView(region)
return TrackContents('hg18', trackViewList)
def extractTrackFromGTrackCore(genome, trackName):
"""
Extract a track from GTracCore
:param genome:
:param trackName:
:return:
"""
trackName = trackName.split(".")[0]
track = Track(trackName.split(":"))
trackViewList = OrderedDict()
for region in genome.regions:
try:
trackViewList[region] = track.getTrackView(region)
except OSError:
# There can be regions that the track does not cover..
# This is a temp fix.. should be bare of the api
pass
return TrackContents(genome, trackViewList)
def _getTrackView(self, trackName, region, allowOverlaps):
track = Track(trackName)
track.addFormatReq(TrackFormatReq(allowOverlaps=allowOverlaps))
return track.getTrackView(region)
def _getTrack(self):
track = Track(self._trackName)
track.addFormatReq(TrackFormatReq(allowOverlaps=self._allowOverlaps))
return track
def _getTrackView(self, trackName, region, allowOverlaps):
track = Track(trackName)
track.addFormatReq(TrackFormatReq(allowOverlaps=allowOverlaps))
return track.getTrackView(region)
def _getTrack(self):
track = Track(self._trackName)
track.addFormatReq(TrackFormatReq(allowOverlaps=self._allowOverlaps))
return track