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 __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 getTrackView(self, region):
#print 'get tv for reg: ',region
#print str(type(self._origRegion)) + " and " + str(type(region))
if Config.USE_SLOW_DEFENSIVE_ASSERTS:
assert (not isIter(self._origRegion) and self._origRegion == region) or \
(isIter(self._origRegion) and region in self._origRegion)
#if self._cachedTV is None:
self._origTrack.addFormatReq(self._trackFormatReq)
origTV = self._origTrack.getTrackView(region)
self._checkTrackFormat(origTV)
assert(not origTV.allowOverlaps)
assert(origTV.borderHandling == 'crop')
assert region == origTV.genomeAnchor
starts, ends, vals, strands, ids, edges, weights, extras = \
self._createRandomizedNumpyArrays(len(origTV.genomeAnchor), origTV.startsAsNumpyArray(), \
origTV.endsAsNumpyArray(), origTV.valsAsNumpyArray(), \
origTV.strandsAsNumpyArray(), origTV.idsAsNumpyArray(), \
origTV.edgesAsNumpyArray(), origTV.weightsAsNumpyArray(), \
origTV.allExtrasAsDictOfNumpyArrays(), origTV.trackFormat, region)
from gtrackcore.util.CommonFunctions import getClassName
self._cachedTV = TrackView(origTV.genomeAnchor, \
(starts + origTV.genomeAnchor.start if starts is not None else None), \
(ends + origTV.genomeAnchor.start if ends is not None else None), \
vals, strands, ids, edges, weights, origTV.borderHandling, origTV.allowOverlaps, extraLists=extras)
assert self._trackFormatReq.isCompatibleWith(self._cachedTV.trackFormat), 'Incompatible track-format: '\
+ str(self._trackFormatReq) + ' VS ' + str(self._cachedTV.trackFormat)
return self._cachedTV
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,
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 _getRawTrackView(self, region, borderHandling, allowOverlaps):
assert len(region) == 1
from collections import OrderedDict
from gtrackcore.track.memmap.CommonMemmapFunctions import findEmptyVal
from gtrackcore.track.core.TrackView import TrackView
import numpy as np
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
self.trackName, region.genome)
prefixList = geSource.getPrefixList()
valDataType = geSource.getValDataType()
valDim = geSource.getValDim()
weightDataType = geSource.getEdgeWeightDataType()
weightDim = geSource.getEdgeWeightDim()
startList, endList, valList, strandList, idList, edgesList, weightsList = [
None
] * 7
extraLists = OrderedDict()
tf = TrackFormat.createInstanceFromPrefixList(prefixList, valDataType, valDim, \
weightDataType, weightDim)
if allowOverlaps and (tf.isDense()
or geSource.hasNoOverlappingElements()):
raise IncompatibleTracksError(prettyPrintTrackName(self.trackName) + ' with format: '\
+ str(tf) + ' does not satisfy ' + str(self._trackFormatReq))
denseAndInterval = tf.isDense() and tf.isInterval()
numEls = 2 if denseAndInterval else 1
if valDataType == 'S':
valDataType = 'S2'
if weightDataType == 'S':
weightDataType = 'S2'
for prefix in prefixList:
if prefix == 'start':
startList = np.array([-1], dtype='int32')
elif prefix == 'end':
if denseAndInterval:
endList = np.array([0, 1], dtype='int32')
else:
endList = np.array([0], dtype='int32')
elif prefix == 'val':
valList = np.array([findEmptyVal(valDataType)] * valDim * numEls, \
dtype=valDataType).reshape((numEls, valDim) if valDim > 1 else numEls)
elif prefix == 'strand':
strandList = np.array([1] * numEls, dtype='int8')
elif prefix == 'id':
idList = np.array([''] * numEls, dtype='S1')
elif prefix == 'edges':
edgesList = np.array([['']] * numEls, dtype='S1')
elif prefix == 'weights':
weightsList = np.array([[[findEmptyVal(weightDataType)]]] * weightDim * numEls, \
dtype=weightDataType).reshape((numEls, 1, weightDim) if weightDim > 1 else (numEls, 1))
else:
extraLists[prefix] = np.array([''] * numEls, dtype='S1')
return TrackView(region, startList, endList, valList, strandList,
idList, edgesList, weightsList, borderHandling,
allowOverlaps, extraLists)
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)
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)
def testInit(self):
starts = [1, 11, 21]
ends = [9, 19, 29]
values = [5.2, -5, 0]
strands = [False, True, False]
ids = ['a1', 'b2', 'c3']
edges = [['b2', 'c3'], ['a1', ''], ['', '']]
weights = [[0.2, 0.3], [-0.1, nan], [nan, nan]]
extras = OrderedDict([('extra1', ['A', 'B', 'C']),
('extra2', ['1.0', '2.0', '3.0'])])
genomeAnchor = GenomeRegion(self.genome, self.chr, 0, 100)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor, [],
ends,
values,
strands,
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts, [],
values,
strands,
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends, [],
strands,
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values, [],
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values,
strands, [],
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values,
strands,
ids, [],
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values,
strands,
ids,
edges, [],
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values,
strands,
ids,
edges,
weights,
'crop',
False,
extraLists=OrderedDict([('extra1', [])]))
t = TrackView(genomeAnchor, None, [0] + ends, [nan] + values, [True] + strands, [''] + ids, [['','']] + edges, [[nan,nan]] + weights, 'crop', False, \
extraLists=OrderedDict([(x,[''] + y) for x,y in extras.items()]))
t = TrackView(genomeAnchor,
starts,
None,
values,
strands,
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
t = TrackView(genomeAnchor,
starts,
ends,
None,
strands,
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
t = TrackView(genomeAnchor,
starts,
ends,
values,
None,
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
t = TrackView(genomeAnchor,
starts,
ends,
values,
strands,
None,
None,
None,
'crop',
False,
extraLists=extras)
t = TrackView(genomeAnchor,
starts,
ends,
values,
strands,
ids,
None,
None,
'crop',
False,
extraLists=extras)
t = TrackView(genomeAnchor,
starts,
ends,
values,
strands,
ids,
edges,
None,
'crop',
False,
extraLists=extras)
t = TrackView(genomeAnchor, starts, ends, values, strands, ids, edges,
weights, 'crop', False)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts[0:-1],
ends,
values,
strands,
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends[0:-1],
values,
strands,
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values[0:-1],
strands,
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values,
strands[0:-1],
ids,
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values,
strands,
ids[0:-1],
edges,
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values,
strands,
ids,
edges[0:-1],
weights,
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values,
strands,
ids,
edges,
weights[0:-1],
'crop',
False,
extraLists=extras)
self.assertRaises(AssertionError,
TrackView,
genomeAnchor,
starts,
ends,
values,
strands,
ids,
edges,
weights,
'crop',
False,
extraLists={'cat': extras['extra1'][0:-1]})
