def testFormats(self):
for start in [None, []]:
for end in [None, []]:
for val in [None, []]:
for strand in [None, []]:
for id, edges, weights in [(None, None, None),
([], None, None),
([], [], None),
([], [], [])]:
for extra in [None, {'a': [], 'b': []}]:
if [] in [start, end, val, edges]:
tf = TrackFormat(start, end, val, strand,
id, edges, weights, extra)
self._assertTrackFormat(tf, start==[], end==[], val==[], strand==[], id==[], edges==[], weights==[], \
hasExtra=extra is not None, extra=extra.keys() if extra is not None else [])
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, genomeAnchor, startList, endList, valList, strandList, idList, edgesList, \
weightsList, borderHandling, allowOverlaps, extraLists=OrderedDict()):
assert startList!=None or endList!=None or valList!=None or edgesList!=None
assert borderHandling in ['crop']
self.genomeAnchor = genomeAnchor.getCopy()
self.trackFormat = TrackFormat(startList, endList, valList, strandList, idList, edgesList, weightsList, extraLists)
self.borderHandling = borderHandling
self.allowOverlaps = allowOverlaps
self._trackElement = TrackElement(self)
#self._bpLevelArray = None
self._startList = startList
self._endList = endList
self._valList = valList
self._strandList = strandList
self._idList = idList
self._edgesList = edgesList
self._weightsList = weightsList
self._extraLists = copy(extraLists)
self._handlePointsAndPartitions()
if self._startList is None:
self._trackElement.start = noneFunc
if self._endList is None:
self._trackElement.end = noneFunc
if self._valList is None:
self._trackElement.val = noneFunc
if self._strandList is None:
self._trackElement.strand = noneFunc
if self._idList is None:
self._trackElement.id = noneFunc
if self._edgesList is None:
self._trackElement.edges = noneFunc
if self._weightsList is None:
self._trackElement.weights = noneFunc
self._updateNumListElements()
for i, list in enumerate([self._startList, self._endList, self._valList, self._strandList, self._idList, self._edgesList, self._weightsList] \
+ [extraList for extraList in self._extraLists.values()]):
assert list is None or len(list) == self._numListElements, 'List (%s): ' % i + str(list) + ' (expected %s elements, found %s)' % (self._numListElements, len(list))
def _assertIsCompatibleWith(self, tfReq, reqList):
for start in [None, []]:
for end in [None, []]:
for val in [None, []]:
for strand in [None, []]:
for id, edges, weights in [(None, None, None),
([], None, None),
([], [], None),
([], [], [])]:
for extra in [None, {'a': [], 'b': []}]:
if [] in [start, end, val]:
tf = TrackFormat(start, end, val, strand,
id, edges, weights, extra)
propList = [tf.isDense(), tf.isValued(), tf.isInterval(), tf.isLinked(), tf.hasStrand(), tf.hasId(), tf.isWeighted(), tf.hasExtra(), \
tf.getValTypeName() if tf.getValTypeName() != '' else False, \
tf.getWeightTypeName() if tf.getWeightTypeName() != '' else False, \
tf.getExtraNames() if tf.getExtraNames() != [] else False]
isCompatible = (not False in [
(r == None or r == p)
for r, p in zip(reqList, propList)
])
self.assertEqual(
isCompatible,
tfReq.isCompatibleWith(tf))
