def runOperation(self):
"""
Run the selected operation.
:return: None
"""
logging.debug(self._args)
logging.debug("Loaded operations: {0}".format(
self._importedOperations.keys()))
operation = self._args.which
if operation == 'list':
self._listTracksInGTrackCore(self._args.genome)
elif operation == 'import':
genome = Genome.createFromJson(self._args.genome)
importTrackIntoGTrack(self._args.name, genome, self._args.path)
elif operation == 'export':
#genome = Genome.createFromJson(self._args.genome)
# fileFormatName = GTrack
exportFile(outFileName=self._args.outName,
genome=self._args.genome,
trackName=self._args.name,
fileFormatName='GTrack',
allowOverlaps=self._args.allowOverlaps)
else:
assert operation in self._importedOperations.keys()
logging.debug("Running operation: {0}".format(operation))
oper = self._importedOperations[operation]
# check args?
a = oper.factory(self._args)
res = a.calculate()
if a.resultIsTrack:
pass
if res is not None and isinstance(res, TrackContents):
# Save result if any
# TODO add support for custom name..
name = a.createTrackName()
logging.debug("Importing track. Name: {0}".format(name))
print(name)
for k,v in res.trackViews.iteritems():
s = v.startsAsNumpyArray()
if s is not None and len(s) > 0:
print(s)
print(type(s))
print(v.endsAsNumpyArray())
print(type(v.endsAsNumpyArray()))
print(v.idsAsNumpyArray())
print(type(v.idsAsNumpyArray()))
print(v.edgesAsNumpyArray())
print(type(v.edgesAsNumpyArray()))
print(v.weightsAsNumpyArray())
print(type(v.weightsAsNumpyArray()))
importTrackFromTrackContents(trackContents=res, trackName=name)
