def _createTrackView(self, starts, ends, vals, strands, ids, edges, weights, extras, sourceRegion, allowOverlaps, sliceFull=False):
genomeAnchor = GenomeRegion(genome=self.genome, chr=self.chr, start=sourceRegion[0], end=sourceRegion[1])
tv = TrackView(genomeAnchor, \
array(starts) if starts is not None else None, \
array(ends) if ends is not None else None, \
array(vals, dtype='float64') if vals is not None else None, \
array(strands) if strands is not None else None, \
array(ids) if ids is not None else None, \
array(edges) if edges is not None else None, \
array(weights) if weights is not None else None, \
'crop', allowOverlaps, \
extraLists=OrderedDict([(key, array(extra)) for key, extra in extras.iteritems()]) if extras is not None else OrderedDict())
if sliceFull:
tv.sliceElementsAccordingToGenomeAnchor()
return tv
def _createTrackView(self, starts, ends, vals, strands, ids, edges, weights, extras, sourceRegion, allowOverlaps, sliceFull=False):
genomeAnchor = GenomeRegion(genome=self.genome, chr=self.chr, start=sourceRegion[0], end=sourceRegion[1])
tv = TrackView(genomeAnchor, \
array(starts) if starts is not None else None, \
array(ends) if ends is not None else None, \
array(vals, dtype='float64') if vals is not None else None, \
array(strands) if strands is not None else None, \
array(ids) if ids is not None else None, \
array(edges) if edges is not None else None, \
array(weights) if weights is not None else None, \
'crop', allowOverlaps, \
extraLists=OrderedDict([(key, array(extra)) for key, extra in extras.iteritems()]) if extras is not None else OrderedDict())
if sliceFull:
tv.sliceElementsAccordingToGenomeAnchor()
return tv
def loadTrackView(trackData, region, borderHandling, allowOverlaps, trackName=[]):
"""
trackData : see TrackSource.getTrackData {'id' : smartmemmap}
region : see GenomeRegion
"""
#brShelve = BoundingRegionShelve(region.genome, trackName, allowOverlaps)
brShelve = trackData.boundingRegionShelve
brInfo = brShelve.getBoundingRegionInfo(region) if brShelve is not None else None
extraArrayNames = [arrayName for arrayName in trackData if arrayName not in \
RESERVED_PREFIXES.keys() + ['leftIndex', 'rightIndex']]
reservedArrays = [TrackViewLoader._getArray(trackData, arrayName, brInfo) for arrayName in RESERVED_PREFIXES]
extraArrays = [TrackViewLoader._getArray(trackData, arrayName, brInfo) for arrayName in extraArrayNames]
trackFormat = TrackFormat( *(reservedArrays + [OrderedDict(zip(extraArrayNames, extraArrays))]) )
if trackFormat.reprIsDense():
if brInfo is None:
leftIndex = region.start
rightIndex = region.end
else:
leftIndex = region.start - brInfo.start
rightIndex = region.end - brInfo.start
else:
leftBin = CompBinManager.getBinNumber(region.start)
rightBin = CompBinManager.getBinNumber(region.end-1)
#leftBin = region.start/COMP_BIN_SIZE
#rightBin = (region.end-1)/COMP_BIN_SIZE
if trackData.get('leftIndex') is None or trackData.get('rightIndex') is None:
raise IOError('Preprocessed track not found. TrackData: ' + ', '.join(trackData.keys()))
leftIndex = TrackViewLoader._getArray(trackData, 'leftIndex', brInfo, leftBin)
rightIndex = TrackViewLoader._getArray(trackData, 'rightIndex', brInfo, rightBin)
slicedReservedArrays = [(array[leftIndex:rightIndex] if array is not None else None) for array in reservedArrays]
slicedExtraArrays = [(array[leftIndex:rightIndex] if array is not None else None) for array in extraArrays]
argList = [region] + slicedReservedArrays + [borderHandling, allowOverlaps] + [OrderedDict(zip(extraArrayNames, slicedExtraArrays))]
tv = TrackView( *(argList) )
if not trackFormat.reprIsDense():
tv.sliceElementsAccordingToGenomeAnchor()
#tv._doScatteredSlicing()
return tv
def loadTrackView(trackData,
region,
borderHandling,
allowOverlaps,
trackName=[]):
"""
trackData : see TrackSource.getTrackData {'id' : smartmemmap}
region : see GenomeRegion
"""
#brShelve = BoundingRegionShelve(region.genome, trackName, allowOverlaps)
brShelve = trackData.boundingRegionShelve
brInfo = brShelve.getBoundingRegionInfo(
region) if brShelve is not None else None
extraArrayNames = [arrayName for arrayName in trackData if arrayName not in \
RESERVED_PREFIXES.keys() + ['leftIndex', 'rightIndex']]
reservedArrays = [
TrackViewLoader._getArray(trackData, arrayName, brInfo)
for arrayName in RESERVED_PREFIXES
]
extraArrays = [
TrackViewLoader._getArray(trackData, arrayName, brInfo)
for arrayName in extraArrayNames
]
trackFormat = TrackFormat(
*(reservedArrays +
[OrderedDict(zip(extraArrayNames, extraArrays))]))
if trackFormat.reprIsDense():
if brInfo is None:
leftIndex = region.start
rightIndex = region.end
else:
leftIndex = region.start - brInfo.start
rightIndex = region.end - brInfo.start
else:
leftBin = CompBinManager.getBinNumber(region.start)
rightBin = CompBinManager.getBinNumber(region.end - 1)
#leftBin = region.start/COMP_BIN_SIZE
#rightBin = (region.end-1)/COMP_BIN_SIZE
if trackData.get('leftIndex') is None or trackData.get(
'rightIndex') is None:
raise IOError('Preprocessed track not found. TrackData: ' +
', '.join(trackData.keys()))
leftIndex = TrackViewLoader._getArray(trackData, 'leftIndex',
brInfo, leftBin)
rightIndex = TrackViewLoader._getArray(trackData, 'rightIndex',
brInfo, rightBin)
slicedReservedArrays = [
(array[leftIndex:rightIndex] if array is not None else None)
for array in reservedArrays
]
slicedExtraArrays = [
(array[leftIndex:rightIndex] if array is not None else None)
for array in extraArrays
]
argList = [region] + slicedReservedArrays + [
borderHandling, allowOverlaps
] + [OrderedDict(zip(extraArrayNames, slicedExtraArrays))]
tv = TrackView(*(argList))
if not trackFormat.reprIsDense():
tv.sliceElementsAccordingToGenomeAnchor()
#tv._doScatteredSlicing()
return tv
