def isMemoBin(region):
if not IS_EXPERIMENTAL_INSTALLATION:
return CompBinManager.isCompBin(region)
if CompBinManager.ALLOW_COMP_BIN_SPLITTING:
isCompBin = CompBinManager.isCompBin(region)
return isCompBin
else:
isChr = not hasattr(region, '__iter__') and any([region.chr, region.start, region.end] == [r.chr, r.start, r.end] \
for r in GenomeInfo.getChrRegs(region.genome))
isChrArm = not hasattr(region, '__iter__') and any([region.chr, region.start, region.end] == [r.chr, r.start, r.end] \
for r in GenomeInfo.getChrArmRegs(region.genome))
return (isChr or isChrArm)
def getGlobalSource(globalSourceStr, genome, minimal):
if minimal == True:
return MinimalBinSource(genome)
elif globalSourceStr == 'test':
return UserBinSource('TestGenome:chr21:10000000-15000000','1000000')
elif globalSourceStr == 'chrs':
return GenomeInfo.getChrRegs(genome)
elif globalSourceStr == 'chrarms':
return GenomeInfo.getChrArmRegs(genome)
elif globalSourceStr == 'ensembl':
return GenomeInfo.getStdGeneRegs(genome)
elif globalSourceStr == 'userbins':
from gold.application.StatRunner import StatJob
assert StatJob.USER_BIN_SOURCE is not None
return StatJob.USER_BIN_SOURCE
#return kwArgs['userBins']
else:
raise ShouldNotOccurError('globalSource not recognized')
def getGlobalSource(globalSourceStr, genome, minimal):
if minimal == True:
return MinimalBinSource(genome)
elif globalSourceStr == 'test':
return UserBinSource('TestGenome:chr21:10000000-15000000',
'1000000')
elif globalSourceStr == 'chrs':
return GenomeInfo.getChrRegs(genome)
elif globalSourceStr == 'chrarms':
return GenomeInfo.getChrArmRegs(genome)
elif globalSourceStr == 'ensembl':
return GenomeInfo.getStdGeneRegs(genome)
elif globalSourceStr == 'userbins':
from gold.application.StatRunner import StatJob
assert StatJob.USER_BIN_SOURCE is not None
return StatJob.USER_BIN_SOURCE
#return kwArgs['userBins']
else:
raise ShouldNotOccurError('globalSource not recognized')
def _getUserBinSource(self, categoryFilterList, forValidation):
return GenomeInfo.getChrArmRegs(self._genome, categoryFilterList)
