def __init__(self, vals=True, strands=True, anchor=None, valDType='float64'):
assert(vals!=True or anchor!=None)
if anchor==None:
numElements = len(vals)
anchor = [10, 10 + numElements]
else:
numElements = anchor[1] - anchor[0]
vals = self._createList(vals, getRandValList(numElements), valDType)
strands = self._createList(strands, getRandStrandList(numElements), 'bool8')
#print (vals, strands, anchor)
TrackView.__init__(self, GenomeRegion('TestGenome', 'chr21', anchor[0], anchor[1]), None, None,
vals, strands, None, None, None, 'crop', False)
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 __init__(self, segments=None, starts=True, ends=True, vals=True, strands=False, ids=False, edges=False, weights=False, \
extras=False, anchor=None, numElements=None, valDType='float64', borderHandling='crop', allowOverlaps=False):
if type(starts) != bool and ends == True:
ends = False
if type(ends) != bool and starts == True:
starts = False
assert not (starts==False and ends==False)
assert segments!=False and segments!=True
assert starts!=None and ends!=None and vals!=None and strands!=None
assert segments==None or (starts==True and ends==True)
assert not (isIter(weights) and not isIter(edges))
assert (any( type(x) not in [bool,type(None)] for x in [segments,starts,ends,vals,strands,ids,edges,weights,extras]) and numElements==None) \
or numElements!=None
#assert(( (type(segments)!=bool or type(starts)!=bool or type(ends)!=bool or \
# type(vals)!=bool or type(strands)!=bool) and numElements==None )\
# or numElements!=None)
#
if anchor==None:
anchor = [10,1000]
if segments != None:
starts = []
ends = []
for seg in segments:
starts.append(seg[0])
ends.append(seg[1])
if isIter(edges):
maxNumEdges = self._findMaxNumEls(edges)
edges = self._appendEmptyToEnd(edges, '', maxNumEdges)
if isIter(weights):
weights = self._appendEmptyToEnd(weights, numpy.nan, maxNumEdges)
[starts, ends, vals, strands, ids, edges, weights] + ([x for x in extras.values()] if isinstance(extras, dict) else [])
for list in [starts, ends, vals, strands, ids, edges, weights] + ([x for x in extras.values()] if isinstance(extras, dict) else []):
if type(list) != bool and numElements == None:
numElements = len(list)
assert(type(list) == bool or len(list) == numElements)
for coordList in [starts, ends]:
if type(coordList) != bool:
for j in range(len(coordList)):
coordList[j] += anchor[0]
randSegmentLists = getRandSegments(numElements, anchor[0], anchor[1])
starts = self._createList(starts, randSegmentLists[0], 'int32')
ends = self._createList(ends, randSegmentLists[1], 'int32')
vals = self._createList(vals, getRandValList(numElements, valDType), valDType)
strands = self._createList(strands, getRandStrandList(numElements), 'bool8')
randIds, randEdges, randWeights = getRandGraphLists(numElements)
ids = self._createList(ids, randIds, randIds.dtype)
edges = self._createList(edges, randEdges, randEdges.dtype)
weights = self._createList(weights, randWeights, 'float64')
if weights is not None and len(weights.shape) == 1:
weights = weights.reshape(weights.shape + (0,))
extras = self._createExtraLists(extras, 'S', numElements)
if starts == None:
if ends[0] != 0:
ends = numpy.append([anchor[0]], ends)
if vals != None:
vals = numpy.append([nan], vals)
if strands != None:
strands = numpy.append([True], strands)
if ends[-1] != anchor[1]:
ends[-1] = anchor[1]
# print (starts, ends, vals, strands, anchor)
TrackView.__init__(self, GenomeRegion('TestGenome', 'chr21', anchor[0], anchor[1]), starts, ends, vals, \
strands, ids, edges, weights, borderHandling, allowOverlaps, extraLists=extras)