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))