def convertDataToWiggle(options, data):
""" the annotWigDict is keyed on chromosome, then on annotationCount,
annotationMax and xAxis. This will be pulled apart by chr keys in the
packData() function.
"""
annotWigDict = {}
for c in data.chrNames:
thisChrNumBins = int(
(float(data.chrLengthsByChrom[c]) / data.genomeLength) *
options.numBins)
annotWigDict[c] = {}
d = annotDataOrNone(data.gffRecordsByChrom, c)
if d is None:
annotWigDict[c]['xAxis'] = numpy.zeros(shape=(thisChrNumBins))
for t in [
'CDS', 'UTR', 'NXE', 'NGE', 'island', 'tandem', 'repeat'
]:
annotWigDict[c][t +
'Count'] = numpy.zeros(shape=(thisChrNumBins))
annotWigDict[c][t + 'Max'] = 0
for i in xrange(0, thisChrNumBins):
annotWigDict[c]['xAxis'][i] = (
(float(i) / (thisChrNumBins - 1.0)) *
float(data.chrLengthsByChrom[c]))
else:
annotWigDict[c] = objListToBinnedWiggle(d,
data.chrLengthsByChrom[c],
thisChrNumBins,
options.gff)
data.annotWigDict = annotWigDict
def convertDataToWiggle( options, data ):
""" the mafWigDict is keyed on chromosome and then
on either maf or xAxis. The dict will be pulled apart
by chromosome in the packData() function.
"""
mafWigDict = {}
for c in data.chrNames:
thisChrNumBins = int( math.floor( ( float( data.chrLengthsByChrom[ c ] ) /
data.genomeLength ) *
options.numBins ))
mafWigDict[ c ] = {}
d = mafDataOrNone( data.mafBlocksByChrom, c )
if d is None:
mafWigDict[ c ] = newMafWigDict( thisChrNumBins )
mafWigDict[ c ] ['xAxis'] = objListUtility_xAxis( data.chrLengthsByChrom[c], thisChrNumBins )
else:
mafWigDict[ c ] = objListToBinnedWiggle( d, data.chrLengthsByChrom[ c ],
thisChrNumBins, options.maf )
data.mafWigDict = mafWigDict
def convertDataToWiggle(options, data):
""" the mafWigDict is keyed on chromosome and then
on either maf or xAxis. The dict will be pulled apart
by chromosome in the packData() function.
"""
mafWigDict = {}
for c in data.chrNames:
thisChrNumBins = int(
math.floor((float(data.chrLengthsByChrom[c]) / data.genomeLength) *
options.numBins))
mafWigDict[c] = {}
d = mafDataOrNone(data.mafBlocksByChrom, c)
if d is None:
mafWigDict[c] = newMafWigDict(thisChrNumBins)
mafWigDict[c]['xAxis'] = objListUtility_xAxis(
data.chrLengthsByChrom[c], thisChrNumBins)
else:
mafWigDict[c] = objListToBinnedWiggle(d, data.chrLengthsByChrom[c],
thisChrNumBins, options.maf)
data.mafWigDict = mafWigDict
def convertDataToWiggle( options, data ):
""" the annotWigDict is keyed on chromosome, then on annotationCount,
annotationMax and xAxis. This will be pulled apart by chr keys in the
packData() function.
"""
annotWigDict = {}
for c in data.chrNames:
thisChrNumBins = int( ( float( data.chrLengthsByChrom[ c ] ) / data.genomeLength ) * options.numBins )
annotWigDict[ c ] = {}
d = annotDataOrNone( data.gffRecordsByChrom, c )
if d is None:
annotWigDict[ c ]['xAxis'] = numpy.zeros( shape = ( thisChrNumBins ))
for t in [ 'CDS', 'UTR', 'NXE', 'NGE', 'island', 'tandem', 'repeat' ]:
annotWigDict[ c ][ t + 'Count' ] = numpy.zeros( shape = ( thisChrNumBins ))
annotWigDict[ c ][ t + 'Max' ] = 0
for i in xrange( 0, thisChrNumBins ):
annotWigDict[c]['xAxis'][ i ] = ((float( i ) / ( thisChrNumBins - 1.0 )) *
float( data.chrLengthsByChrom[ c ] ) )
else:
annotWigDict[ c ] = objListToBinnedWiggle( d, data.chrLengthsByChrom[ c ], thisChrNumBins, options.gff )
data.annotWigDict = annotWigDict