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._doneCalculatingTrackViewBasedValues = False
self._fixedLength = None
self._fixedGapSize = None
self._reprIsDense = None
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, fn, *args, **kwArgs):
GenomeElementSource.__init__(self, fn, *args, **kwArgs)
f = open(fn)
possibleHeader = f.readline()
if possibleHeader.startswith('track'):
self._numHeaderLines = 1
self._numCols = None
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,
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 __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()
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, 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 __init__(self, fn, *args, **kwArgs):
GenomeElementSource.__init__(self, fn, *args, **kwArgs)
self._initAll()
self._handleTrackDefinitionLineIfPresent(self._getFile().readline())
self._parseFirstDeclarationLine()
def __init__(self, *args, **kwArgs):
GenomeElementSource.__init__(self, *args, **kwArgs)
self._returnedOneElement = False
def __init__(self, *args, **kwArgs):
GenomeElementSource.__init__(self, *args, **kwArgs)
self._boundingRegionTuples = []
self._chr = None
def __init__(self, *args, **kwArgs):
GenomeElementSource.__init__(self, *args, **kwArgs)
self._boundingRegionTuples = []
if self._getFile().read(1) != '>':
raise InvalidFormatError('FASTA file does not start with the ">" character.')
def __init__(self, *args, **kwArgs):
GenomeElementSource.__init__(self, *args, **kwArgs)
self._returnedOneElement = False
def __init__(self, *args, **kwArgs):
GenomeElementSource.__init__(self, *args, **kwArgs)
self._boundingRegionTuples = []
self._chr = None
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, geSource, genome=None):
from gtrackcore.input.wrappers.GEDependentAttributesHolder import GEDependentAttributesHolder
geSource = GEDependentAttributesHolder(geSource)
GESourceWrapper.__init__(self, geSource)
GenomeElementSource.__init__(self, '', genome=genome)
def __init__(self, geSource, genome=None):
from gtrackcore.input.wrappers.GEDependentAttributesHolder import GEDependentAttributesHolder
geSource = GEDependentAttributesHolder(geSource)
GESourceWrapper.__init__(self, geSource)
GenomeElementSource.__init__(self, '', genome=genome)
def __init__(self, fn, *args, **kwArgs):
GenomeElementSource.__init__(self, fn, *args, **kwArgs)
self._initAll()
self._handleTrackDefinitionLineIfPresent(self._getFile().readline())
self._parseFirstDeclarationLine()
