def __init__(self, geSource):
self._geSource = self._decorateGESource(geSource)
self._boundingRegionsAndGEsCorresponds = None
self._areValsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getValTypeName() == 'Category'
self._areEdgeWeightsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getWeightTypeName() == 'Category'
self._valCategories = set()
self._edgeWeightCategories = set()
self._numElements = OrderedDefaultDict(int)
self._maxStrLens = OrderedDefaultDict(partial(self._initMaxStrLens, self._getMaxStrLensKeys()))
self._maxNumEdges = OrderedDefaultDict(int)
self._hasCalculatedStats = False
def __init__(self, geSource):
self._geSource = self._decorateGESource(geSource)
self._boundingRegionsAndGEsCorrespond = None
self._areValsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getValTypeName() == 'Category'
self._areEdgeWeightsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getWeightTypeName() == 'Category'
self._valCategories = set()
self._edgeWeightCategories = set()
self._numElements = OrderedDefaultDict(int)
self._maxStrLens = OrderedDefaultDict(partial(self._initMaxStrLens, self._getMaxStrLensKeys()))
self._maxNumEdges = OrderedDefaultDict(int)
self._hasCalculatedStats = False
class GESourceManager(object):
def __init__(self, geSource):
self._geSource = self._decorateGESource(geSource)
self._boundingRegionsAndGEsCorresponds = None
self._areValsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getValTypeName() == 'Category'
self._areEdgeWeightsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getWeightTypeName() == 'Category'
self._valCategories = set()
self._edgeWeightCategories = set()
self._numElements = OrderedDefaultDict(int)
self._maxStrLens = OrderedDefaultDict(partial(self._initMaxStrLens, self._getMaxStrLensKeys()))
self._maxNumEdges = OrderedDefaultDict(int)
self._hasCalculatedStats = False
# self._calcStatisticsInExtraPass()
def _decorateGESource(self, geSource):
return GEDependentAttributesHolder(geSource)
def _getMaxStrLensKeys(self):
prefixSet = set(self._geSource.getPrefixList())
return (['val'] if 'val' in prefixSet and self._geSource.getValDataType() == 'S' else []) + \
(['id'] if 'id' in prefixSet else []) + \
(['edges'] if 'edges' in prefixSet else []) + \
(['weights'] if 'weights' in prefixSet and self._geSource.getEdgeWeightDataType() == 'S' else []) + \
[x for x in prefixSet if x not in RESERVED_PREFIXES]
@staticmethod
def _initMaxStrLens(keys):
return dict([(x,0) for x in keys])
def _calcStatisticsInExtraPass(self):
if not self._hasCalculatedStats:
prevPrintWarnings = self._geSource.getPrintWarnings()
self._geSource.setPrintWarnings(False)
for el in self._geSource:
chr = el.chr
self._numElements[chr] += 1
if el.isBlankElement:
continue
if self._areValsCategorical:
self._valCategories.add(el.val)
if self._areEdgeWeightsCategorical:
self._edgeWeightCategories |= set(el.weights)
for prefix in self._maxStrLens[chr]:
content = getattr(el, prefix, None)
if content is not None:
self._maxStrLens[chr][prefix] = \
max( self._maxStrLens[chr][prefix], \
max(1, len(content)) if isinstance(content, basestring) else \
max([1] + [len(x) for x in flatten(content)]) )
if prefix == 'edges':
self._maxNumEdges[chr] = max(self._maxNumEdges[chr], len(el.edges))
self._geSource.setPrintWarnings(prevPrintWarnings)
self._hasCalculatedStats = True
def getGESource(self):
return self._geSource
def getBoundingRegionTuples(self):
boundingRegionTuples = [x for x in self._getBoundingRegionTuples() \
if x.region.chr is not None]
if len(boundingRegionTuples) == 0:
from gtrackcore.input.core.GenomeElementSource import BoundingRegionTuple
from gtrackcore.track.core.GenomeRegion import GenomeRegion
from gtrackcore.metadata.GenomeInfo import GenomeInfo
geChrList = self.getAllChrs()
boundingRegionTuples = [BoundingRegionTuple( \
GenomeRegion(chr=chr, start=0, end=GenomeInfo.getChrLen(self._geSource.genome, chr)), \
self.getNumElementsForChr(chr) ) \
for chr in geChrList]
self._boundingRegionsAndGEsCorresponds = False
else:
self._boundingRegionsAndGEsCorresponds = True
return boundingRegionTuples
def _getBoundingRegionTuples(self):
return self._geSource.getBoundingRegionTuples()
def boundingRegionsAndGEsCorresponds(self):
assert self._boundingRegionsAndGEsCorresponds is not None
return self._boundingRegionsAndGEsCorresponds
def getPrefixList(self):
return self._geSource.getPrefixList()
def getValDataType(self):
return self._geSource.getValDataType()
def getValDim(self):
return self._geSource.getValDim()
def getEdgeWeightDataType(self):
return self._geSource.getEdgeWeightDataType()
def getEdgeWeightDim(self):
return self._geSource.getEdgeWeightDim()
def isSorted(self):
return self._geSource.isSorted()
def getAllChrs(self):
self._calcStatisticsInExtraPass()
return self._numElements.keys()
def getNumElements(self):
self._calcStatisticsInExtraPass()
return sum(self._numElements.values())
def getNumElementsForChr(self, chr):
self._calcStatisticsInExtraPass()
return self._numElements[chr]
def getValCategories(self):
self._calcStatisticsInExtraPass()
return self._valCategories
def getEdgeWeightCategories(self):
self._calcStatisticsInExtraPass()
return self._edgeWeightCategories
def getMaxNumEdges(self):
self._calcStatisticsInExtraPass()
return max(self._maxNumEdges.values())
def getMaxNumEdgesForChr(self, chr):
self._calcStatisticsInExtraPass()
return self._maxNumEdges[chr]
def getMaxStrLens(self):
self._calcStatisticsInExtraPass()
reduce(lambda x,y:dict((key, max(x[key], y[key])) for key in x.keys()), \
self._maxStrLens.values())
def getMaxStrLensForChr(self, chr):
self._calcStatisticsInExtraPass()
return self._maxStrLens[chr]
class GESourceManager(object):
def __init__(self, geSource):
self._geSource = self._decorateGESource(geSource)
self._boundingRegionsAndGEsCorrespond = None
self._areValsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getValTypeName() == 'Category'
self._areEdgeWeightsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getWeightTypeName() == 'Category'
self._valCategories = set()
self._edgeWeightCategories = set()
self._numElements = OrderedDefaultDict(int)
self._maxStrLens = OrderedDefaultDict(partial(self._initMaxStrLens, self._getMaxStrLensKeys()))
self._maxNumEdges = OrderedDefaultDict(int)
self._hasCalculatedStats = False
# self._calcStatisticsInExtraPass()
def _decorateGESource(self, geSource):
return GEDependentAttributesHolder(geSource)
def _getMaxStrLensKeys(self):
prefixSet = set(self._geSource.getPrefixList())
return (['val'] if 'val' in prefixSet and self._geSource.getValDataType() == 'S' else []) + \
(['id'] if 'id' in prefixSet else []) + \
(['edges'] if 'edges' in prefixSet else []) + \
(['weights'] if 'weights' in prefixSet and self._geSource.getEdgeWeightDataType() == 'S' else []) + \
[x for x in prefixSet if x not in RESERVED_PREFIXES]
@staticmethod
def _initMaxStrLens(keys):
return dict([(x,0) for x in keys])
def _calcStatisticsInExtraPass(self):
if not self._hasCalculatedStats:
prevPrintWarnings = self._geSource.getPrintWarnings()
self._geSource.setPrintWarnings(False)
if self._geSource.isSliceSource():
if len(self._getMaxStrLensKeys()):
raise NotImplementedError('Dimension calculation not yet implemented for slice-based GenomeElementSources.')
prefixList = self._geSource.getPrefixList()
for el in self._geSource:
chr = el.chr
self._numElements[chr] += len(getattr(el, prefixList[0]))
else:
for el in self._geSource:
chr = el.chr
self._numElements[chr] += 1
if el.isBlankElement:
continue
if self._areValsCategorical:
self._valCategories.add(el.val)
if self._areEdgeWeightsCategorical:
self._edgeWeightCategories |= set(el.weights)
for prefix in self._maxStrLens[chr]:
content = getattr(el, prefix, None)
if content is not None:
self._maxStrLens[chr][prefix] = \
max( self._maxStrLens[chr][prefix], \
max(1, len(content)) if isinstance(content, basestring) else \
max([1] + [len(x) for x in flatten(content)]) )
if prefix == 'edges':
self._maxNumEdges[chr] = max(self._maxNumEdges[chr], len(el.edges))
self._geSource.setPrintWarnings(prevPrintWarnings)
self._hasCalculatedStats = True
def getGESource(self):
return self._geSource
def getBoundingRegionTuples(self):
boundingRegionTuples = [x for x in self._getBoundingRegionTuples() \
if x.region.chr is not None]
if len(boundingRegionTuples) == 0:
from gtrackcore.input.core.GenomeElementSource import BoundingRegionTuple
from gtrackcore.track.core.GenomeRegion import GenomeRegion
from gtrackcore.metadata.GenomeInfo import GenomeInfo
geChrList = self.getAllChrs()
boundingRegionTuples = [BoundingRegionTuple( \
GenomeRegion(chr=chr, start=0, end=GenomeInfo.getChrLen(self._geSource.genome, chr)), \
self.getNumElementsForChr(chr) ) \
for chr in geChrList]
self._boundingRegionsAndGEsCorrespond = False
else:
self._boundingRegionsAndGEsCorrespond = True
return boundingRegionTuples
def _getBoundingRegionTuples(self):
return self._geSource.getBoundingRegionTuples()
def boundingRegionsAndGEsCorrespond(self):
assert self._boundingRegionsAndGEsCorrespond is not None
return self._boundingRegionsAndGEsCorrespond
def getPrefixList(self):
return self._geSource.getPrefixList()
def getValDataType(self):
return self._geSource.getValDataType()
def getValDim(self):
return self._geSource.getValDim()
def getEdgeWeightDataType(self):
return self._geSource.getEdgeWeightDataType()
def getEdgeWeightDim(self):
return self._geSource.getEdgeWeightDim()
def isSorted(self):
return self._geSource.isSorted()
def getAllChrs(self):
self._calcStatisticsInExtraPass()
return self._numElements.keys()
def getNumElements(self):
self._calcStatisticsInExtraPass()
return sum(self._numElements.values())
def getNumElementsForChr(self, chr):
self._calcStatisticsInExtraPass()
return self._numElements[chr]
def getValCategories(self):
self._calcStatisticsInExtraPass()
return self._valCategories
def getEdgeWeightCategories(self):
self._calcStatisticsInExtraPass()
return self._edgeWeightCategories
def getMaxNumEdges(self):
self._calcStatisticsInExtraPass()
return max(self._maxNumEdges.values())
def getMaxNumEdgesForChr(self, chr):
self._calcStatisticsInExtraPass()
return self._maxNumEdges[chr]
def getMaxStrLens(self):
self._calcStatisticsInExtraPass()
return reduce(lambda x,y:dict((key, max(x[key], y[key])) for key in x.keys()), \
self._maxStrLens.values())
def getMaxStrLensForChr(self, chr):
self._calcStatisticsInExtraPass()
return self._maxStrLens[chr]
def getMaxChrStrLen(self):
self._calcStatisticsInExtraPass()
return max(len(chr) for chr in self._maxStrLens.keys())