def _commonTestComposer(self, withTrackGESource, composerCls, suffix):
geSourceTest = self._commonSetup()
for caseName in geSourceTest.cases:
if not (caseName == suffix or \
(caseName.startswith(suffix) and caseName[len(suffix)] in ['_','.'])):
continue
if 'no_print' in caseName or \
withTrackGESource and ('no_track_extract' in caseName or \
caseName.endswith('_no_hb')):
print 'Test case skipped: ' + caseName
continue
print caseName
case = geSourceTest.cases[caseName]
testFn = self._writeTestFile(case)
sourceClass = case.sourceClass if case.sourceClass is not None else GenomeElementSource
genome = self.GENOME if withTrackGESource else case.genome
rawCaseGESource = sourceClass(testFn, genome, printWarnings=False)
caseGESource = GEDependentAttributesHolder(rawCaseGESource)
#actualSourceClass = caseGESource._geSource.__class__
if withTrackGESource:
for x in caseGESource:
pass
boundingRegionTuples = caseGESource.getBoundingRegionTuples()
boundingRegions = [br.region for br in boundingRegionTuples]
if boundingRegions == [] or all(br.chr is None for br in boundingRegions):
boundingRegions = GlobalBinSource(self.GENOME)
trackName = self.TRACK_NAME_PREFIX + case.trackName
self._preProcess(trackName)
allowOverlaps = True if ('start' in case.prefixList) and not caseName.endswith('_compose_no_overlaps') else False
inputGESource = TrackGenomeElementSource(self.GENOME, trackName, boundingRegions, \
printWarnings=False, allowOverlaps=allowOverlaps)
else:
inputGESource = rawCaseGESource
composer = composerCls(inputGESource)
contents = composer.returnComposed()
print contents
composedFile = NamedTemporaryFile('w', suffix='.' + suffix)
composedFile.write(contents)
composedFile.flush()
#print actualSourceClass.__name__
outputGESource = GEDependentAttributesHolder(sourceClass(composedFile.name, genome, printWarnings=False))
if 'no_check_print' in caseName or withTrackGESource and 'no_check_track_extract' in caseName:
print 'No checks for case: ' + caseName
else:
caseGEs = [ge.getCopy() for ge in caseGESource]
outputGEs = [ge.getCopy() for ge in outputGESource]
isSortableGE = any(getattr(caseGEs[0], x) is not None for x in ['start','end']) if len(caseGEs) > 0 else False
if withTrackGESource and isSortableGE and not caseGESource.hasBoundingRegionTuples():
caseGEs = sorted(caseGEs)
self.assertGenomeElementLists(caseGEs, outputGEs)
self.assertListsOrDicts(caseGESource.getBoundingRegionTuples(), outputGESource.getBoundingRegionTuples())
