def _compute(self):
kwArgs = copy(self._kwArgs)
if 'rawStatistic' in kwArgs:
del kwArgs['rawStatistic']
matrixElRes = []
tr1Subtypes = ProcTrackOptions.getSubtypes(self.getGenome(), self._track.trackName, True)
assert len(tr1Subtypes) > 0
for subtype1 in tr1Subtypes:#['0','1']:
for subtype2 in ['0','1']:
tn1 = self._track.trackName + [subtype1]
tn2 = self._track2.trackName + [subtype2]
if not os.path.exists(createDirPath(tn1,self.getGenome())) or not os.path.exists(createDirPath(tn2,self.getGenome())):
raise IncompatibleTracksError
#print ','
track1 = Track( tn1)
track1.formatConverters = self._track.formatConverters
track2 = Track( tn2)
track2.formatConverters = self._track2.formatConverters
#self._addChild(self._rawStatistic(self._region, track1, track2, **kwArgs) )
matrixElRes.append( self._rawStatistic(self._region, track1, track2, **kwArgs).getResult() )
ResultsMemoizer.flushStoredResults()
#assert len(self._children) == 7
#return dict(zip( '00,01,10,11'.split(','), [x.getResult() for x in self._children[3:]]))
allChildRes = array(matrixElRes)
#allChildRes = array([x.getResult() for x in self._children[3:]])
allChildRes = allChildRes.reshape((-1,2))
return OrderedDict([('Matrix', allChildRes.tolist()), ('Rows', tr1Subtypes), ('Cols', ['Case','Control'])])
def _compute(self):
kwArgs = copy(self._kwArgs)
if 'rawStatistic' in kwArgs:
del kwArgs['rawStatistic']
matrixElRes = []
tr1Subtypes = ProcTrackOptions.getSubtypes(self.getGenome(),
self._track.trackName, True)
tr2Subtypes = ProcTrackOptions.getSubtypes(self.getGenome(),
self._track2.trackName,
True)
assert len(tr1Subtypes) > 0, str(self._track.trackName)
assert len(tr2Subtypes) > 0, str(self._track2.trackName)
if 'minimal' in self._kwArgs:
tr1Subtypes = tr1Subtypes[:1]
tr2Subtypes = tr2Subtypes[:1]
for subtype1 in tr1Subtypes: #['0','1']:
#for subtype2 in ['0','1']:
for subtype2 in tr2Subtypes:
# print ','
tn1 = self._track.trackName + [subtype1]
tn2 = self._track2.trackName + [subtype2]
if not os.path.exists(createDirPath(
tn1, self.getGenome())) or not os.path.exists(
createDirPath(tn2, self.getGenome())):
raise IncompatibleTracksError
#print ','
track1 = Track(tn1)
track1.formatConverters = self._track.formatConverters
track2 = Track(tn2)
track2.formatConverters = self._track2.formatConverters
#self._addChild(self._rawStatistic(self._region, track1, track2, **kwArgs) )
matrixElRes.append(
self._rawStatistic(self._region, track1, track2,
**kwArgs).getResult())
ResultsMemoizer.flushStoredResults()
#assert len(self._children) == 7
#return dict(zip( '00,01,10,11'.split(','), [x.getResult() for x in self._children[3:]]))
allChildRes = array(matrixElRes)
#allChildRes = array([x.getResult() for x in self._children[3:]])
allChildRes = allChildRes.reshape((len(tr1Subtypes), len(tr2Subtypes)))
return {
'Result':
OrderedDict([('Matrix', allChildRes.tolist()),
('Rows', tr1Subtypes), ('Cols', tr2Subtypes)])
}
def _createChildren(self):
kwArgs = copy(self._kwArgs)
if 'rawStatistic' in kwArgs:
del kwArgs['rawStatistic']
track2 = self._track2 if hasattr(self, '_track2') else None
self._addChild(
FormatSpecStat(self._region, self._track,
TrackFormatReq(dense=False, val='tc')))
#self._track.formatConverters = 'Dummy' #to avoid check of tracks not being used..
#self._track2.formatConverters = 'Dummy' #to avoid check of tracks not being used..
#self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(dense=False, val='tc') ) )
self._addChild(
self._rawStatistic(
self._region, self._track, track2, **
kwArgs)) #This will actually compute, without any use for it.
self._indexOfFirstSubCatChild = len(self._children)
for subtype1 in ['0', '1']:
#for subtype2 in ['0','1']:
tn1 = self._track.trackName + [subtype1]
if not os.path.exists(createDirPath(tn1, self.getGenome())):
#logMessage('DID NOT EXIST.. '+createOrigPath(self.getGenome(),tn1))
raise IncompatibleTracksError
#else:
# logMessage('DID EXIST')
track1 = Track(tn1)
track1.formatConverters = self._track.formatConverters
#track2 = Track( self._track2.trackName + [subtype2])
#track2.formatConverters = self._track2.formatConverters
self._addChild(
self._rawStatistic(self._region, track1, track2, **kwArgs))
def _createChildren(self):
kwArgs = copy(self._kwArgs)
if 'rawStatistic' in kwArgs:
del kwArgs['rawStatistic']
track2 = self._track2 if hasattr(self, '_track2') else None
self._addChild( FormatSpecStat(self._region, self._track, TrackFormatReq(dense=False, val='tc') ) )
#self._track.formatConverters = 'Dummy' #to avoid check of tracks not being used..
#self._track2.formatConverters = 'Dummy' #to avoid check of tracks not being used..
#self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(dense=False, val='tc') ) )
self._addChild( self._rawStatistic(self._region, self._track, track2, **kwArgs) ) #This will actually compute, without any use for it.
self._indexOfFirstSubCatChild = len(self._children)
for subtype1 in ['0','1']:
#for subtype2 in ['0','1']:
tn1 = self._track.trackName + [subtype1]
if not os.path.exists(createDirPath(tn1, self.getGenome())):
#logMessage('DID NOT EXIST.. '+createOrigPath(self.getGenome(),tn1))
raise IncompatibleTracksError
#else:
# logMessage('DID EXIST')
track1 = Track( tn1)
track1.formatConverters = self._track.formatConverters
#track2 = Track( self._track2.trackName + [subtype2])
#track2.formatConverters = self._track2.formatConverters
self._addChild(self._rawStatistic(self._region, track1, track2, **kwArgs) )
def _createChildren(self):
kwArgs = copy(self._kwArgs)
if 'rawStatistic' in kwArgs:
del kwArgs['rawStatistic']
self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(dense=False, val='tc') ) )
self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(dense=False, val='tc') ) )
self._addChild( self._rawStatistic(self._region, self._track, self._track2, **kwArgs) )
#try:
for subtype1 in ['0','1']:
for subtype2 in ['0','1']:
tn1 = self._track.trackName + [subtype1]
tn2 = self._track2.trackName + [subtype2]
if not os.path.exists(createDirPath(tn1, self.getGenome())) or not os.path.exists(createDirPath(tn2,self.getGenome())):
raise IncompatibleTracksError
track1 = Track( tn1)
track1.formatConverters = self._track.formatConverters
track2 = Track( tn2)
track2.formatConverters = self._track2.formatConverters
self._addChild(self._rawStatistic(self._region, track1, track2, **kwArgs) )
def _createChildren(self):
kwArgs = copy(self._kwArgs)
if 'rawStatistic' in kwArgs:
del kwArgs['rawStatistic']
self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(dense=False, val='tc') ) )
self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(dense=False, val='tc') ) )
self._addChild( self._rawStatistic(self._region, self._track, self._track2, **kwArgs) )
#try:
for subtype1 in ['0','1']:
for subtype2 in ['0','1']:
tn1 = self._track.trackName + [subtype1]
tn2 = self._track2.trackName + [subtype2]
if not os.path.exists(createDirPath(tn1, self.getGenome())) or not os.path.exists(createDirPath(tn2,self.getGenome())):
raise IncompatibleTracksError
track1 = Track( tn1)
track1.formatConverters = self._track.formatConverters
track2 = Track( tn2)
track2.formatConverters = self._track2.formatConverters
self._addChild(self._rawStatistic(self._region, track1, track2, **kwArgs) )