def __init__(self, fn, *args, **kwArgs): GenomeElementSource.__init__(self, fn, *args, **kwArgs) f = open(fn) trackDef = f.readline() if trackDef.startswith("track type=bedGraph"): numHeaderLines = 1 else: numHeaderLines = 0 headerLine = f.readline() while headerLine.startswith("#"): numHeaderLines += 1 headerLine = f.readline() self._numHeaderLines = numHeaderLines
def __init__(self, fn, *args, **kwArgs): GenomeElementSource.__init__(self, fn, *args, **kwArgs) f = open(fn) trackDef = f.readline().replace('\'','"') if not trackDef.startswith('track type="array"'): raise InvalidFormatError('Track definition line must start with: track type="array". Line: ' + trackDef) header = self._parseHeader(trackDef) if not all(key in header for key in ['expScale', 'expStep', 'expNames']): raise InvalidFormatError('Track definition line must define values for expScale, expStep and expNames: ' + trackDef) expNames = header['expNames'] if not all(expNames[i] == '"' for i in [0,-1]): raise InvalidFormatError('expNames does not start and end in quote marks: ' + trackDef) self._globExpCount = len( [x for x in expNames[1:-2].split(',') if x != ''] ) if self._globExpCount < 3: raise InvalidFormatError('Microarray data must have at least 3 experiments. Length of expNames: ' + str(self._globExpCount))
def __init__( self, genome, trackName, boundingRegions, globalCoords=True, allowOverlaps=False, printWarnings=True, *args, **kwArgs ): assert len(boundingRegions) > 0 GenomeElementSource.__init__( self, "", genome=genome, trackName=trackName, printWarnings=printWarnings, *args, **kwArgs ) self._boundingRegions = boundingRegions self._isSorted = all([x == y for x, y in zip(boundingRegions, sorted(boundingRegions))]) self._boundingRegionTuples = None self._allowOverlaps = allowOverlaps self._globalCoords = globalCoords self._prefixList = None self._valDataType = "float64" self._valDim = 1 self._edgeWeightDataType = "float64" self._edgeWeightDim = 1 self._foundDataTypesAndDims = False self._fileType = None self._preProcVersion = None self._id = None self._undirectedEdges = None self._foundTrackInfoBasedMetaData = False self._fixedLength = None self._fixedGapSize = None self._reprIsDense = None
def __init__(self, genome, trackName, region, valSlice, valDataType='float64'): GenomeElementSource.__init__(self, None, genome=genome, trackName=trackName) self._returnedOneElement = False self._valSlice = valSlice self._region = region self._valDataType = valDataType
def getPrefixList(self): return GenomeElementSource.getPrefixList(self)
def parseFirstDataLine(self): return GenomeElementSource.parseFirstDataLine(self)
def __init__(self, geSource, genome=None): from gtrackcore_memmap.input.wrappers.GEDependentAttributesHolder import GEDependentAttributesHolder geSource = GEDependentAttributesHolder(geSource) GESourceWrapper.__init__(self, geSource) GenomeElementSource.__init__(self, '', genome=genome)
def _getStrandFromString(cls, val): if val == '?': return BINARY_MISSING_VAL else: return GenomeElementSource._getStrandFromString(val)
def __init__(self, *args, **kwArgs): GenomeElementSource.__init__(self, *args, **kwArgs) self._boundingRegionTuples = [] self._chr = None
def _checkBoundingRegionSortedPair(self, lastBoundingRegion, br): GenomeElementSource._checkBoundingRegionSortedPair(self, lastBoundingRegion, br) if br.start is not None and br.end is not None: if lastBoundingRegion.end == br.start: raise InvalidFormatError("Error: bounding regions '%s' and '%s' are adjoining (there is no gap between them)." % (lastBoundingRegion, br))
def __init__(self, fn, *args, **kwArgs): GenomeElementSource.__init__(self, fn, *args, **kwArgs) self._initAll() self._handleTrackDefinitionLineIfPresent(self._getFile().readline()) self._parseFirstDeclarationLine()
def __init__(self, windowSource, genome, trackName, chr, func): GenomeElementSource.__init__(self, None, genome=genome, trackName=trackName) self._windowSource = windowSource self._windowIter = None self._genomeElement.chr = chr self._func = func
def __init__(self, *args, **kwArgs): GenomeElementSource.__init__(self, *args, **kwArgs) self._returnedOneElement = False