def _commonComplementGtrackFile(origFn, dbFn, intersectingFactor,
gtrackColsToAdd, genome):
origGESource = GtrackGenomeElementSource(origFn, genome)
dbGESource = GtrackGenomeElementSource(dbFn, genome)
dbPrefixes = dbGESource.getPrefixList()
if intersectingFactor == 'id':
fullDbDict = IdFullInfoDict(dbGESource, dbPrefixes)
elif intersectingFactor == 'position':
fullDbDict = TupleFullInfoDict(dbGESource, dbPrefixes)
else:
ShouldNotOccurError
forcedHeaderDict = {}
dbHeaderDict = dbGESource.getHeaderDict()
if 'value' in gtrackColsToAdd:
forcedHeaderDict['value type'] = dbHeaderDict['value type']
forcedHeaderDict['value dimension'] = dbHeaderDict['value dimension']
if 'edges' in gtrackColsToAdd:
forcedHeaderDict['edge weight type'] = dbHeaderDict['edge weight type']
forcedHeaderDict['edge weight dimension'] = dbHeaderDict[
'edge weight dimension']
composerCls = ExtendedGtrackComposer if origGESource.isExtendedGtrackFile(
) else StdGtrackComposer
composedFile = composerCls( ElementComplementer(origGESource, fullDbDict, gtrackColsToAdd), \
forcedHeaderDict=forcedHeaderDict).returnComposed()
return expandHeadersOfGtrackFileAndReturnComposer(
'', genome, strToUseInsteadOfFn=composedFile)
def _commonComplementGtrackFile(origFn, dbFn, intersectingFactor, gtrackColsToAdd, genome):
origGESource = GtrackGenomeElementSource(origFn, genome)
dbGESource = GtrackGenomeElementSource(dbFn, genome)
dbPrefixes = dbGESource.getPrefixList()
if intersectingFactor == 'id':
fullDbDict = IdFullInfoDict(dbGESource, dbPrefixes)
elif intersectingFactor == 'position':
fullDbDict = TupleFullInfoDict(dbGESource, dbPrefixes)
else:
ShouldNotOccurError
forcedHeaderDict = {}
dbHeaderDict = dbGESource.getHeaderDict()
if 'value' in gtrackColsToAdd:
forcedHeaderDict['value type'] = dbHeaderDict['value type']
forcedHeaderDict['value dimension'] = dbHeaderDict['value dimension']
if 'edges' in gtrackColsToAdd:
forcedHeaderDict['edge weight type'] = dbHeaderDict['edge weight type']
forcedHeaderDict['edge weight dimension'] = dbHeaderDict['edge weight dimension']
composerCls = ExtendedGtrackComposer if origGESource.isExtendedGtrackFile() else StdGtrackComposer
composedFile = composerCls( ElementComplementer(origGESource, fullDbDict, gtrackColsToAdd), \
forcedHeaderDict=forcedHeaderDict).returnComposed()
return expandHeadersOfGtrackFileAndReturnComposer('', genome, strToUseInsteadOfFn=composedFile)
def _commonStandardizeGtrackFile(fn, genome, suffix=None):
geSource = GenomeElementSource(fn, genome, suffix=suffix)
composedFile = StdGtrackComposer(
GtrackElementStandardizer(geSource)).returnComposed()
return expandHeadersOfGtrackFileAndReturnComposer(
'', genome, strToUseInsteadOfFn=composedFile)
def _commonStandardizeGtrackFile(fn, genome, suffix=None):
geSource = GenomeElementSource(fn, genome, suffix=suffix)
composedFile = StdGtrackComposer( GtrackElementStandardizer(geSource)).returnComposed()
return expandHeadersOfGtrackFileAndReturnComposer('', genome, strToUseInsteadOfFn=composedFile)