def preProcFilesExist(cls, genome, trackName, allowOverlaps):
collector = PreProcMetaDataCollector(genome, trackName)
preProcFilesExist = collector.preProcFilesExist(allowOverlaps)
if preProcFilesExist is None:
merged = cls.mergedPreProcFilesExist(genome, trackName,
allowOverlaps)
if merged:
preProcFilesExist = True
else:
preProcFilesExist = cls.oldTypePreProcFilesExist(
genome, trackName, allowOverlaps)
collector.updatePreProcFilesExistFlag(allowOverlaps,
preProcFilesExist, merged)
return preProcFilesExist
def preProcFilesExist(genome, trackName, allowOverlaps):
collector = PreProcMetaDataCollector(genome, trackName)
preProcFilesExist = collector.preProcFilesExist(allowOverlaps)
if preProcFilesExist is None:
dirPath = createDirPath(trackName, genome, allowOverlaps=allowOverlaps)
if BoundingRegionShelve(genome, trackName, allowOverlaps).fileExists():
preProcFilesExist = True
# any( fn.split('.')[0] in ['start', 'end', 'val', 'edges'] \
# for fn in os.listdir(dirPath) if os.path.isfile(os.path.join(dirPath, fn)) )
else:
if os.path.exists(dirPath):
preProcFilesExist = PreProcessUtils._hasOldTypeChromSubDirs(dirPath, genome)
else:
preProcFilesExist = False
collector.updatePreProcFilesExistFlag(allowOverlaps, preProcFilesExist)
return preProcFilesExist
def process(self):
assert self._genome is not None, 'Error: genome must be specified when preprocessing tracks.'
atLeastOneFinalized = False
for trackName in self._allTrackNames():
assert trackName != ['']
overlapRulesProcessedForTrackName = []
collector = PreProcMetaDataCollector(self._genome, trackName)
try:
trackName = self._renameTrackNameIfIllegal(trackName)
for allowOverlaps in [True, False]:
anyGeSourceManagers = False
for geSourceManager in self._allGESourceManagers(
trackName, allowOverlaps):
anyGeSourceManagers = True
# PreProcess if needed
if self._shouldPreProcess():
PreProcessUtils.removeOutdatedPreProcessedFiles(
self._genome, trackName, allowOverlaps,
self._mode)
if self._shouldPrintProcessMessages(
) and allowOverlaps not in overlapRulesProcessedForTrackName:
self._printProcessTrackMessage(
trackName, allowOverlaps)
overlapRulesProcessedForTrackName.append(
allowOverlaps)
self._status = 'Trying to preprocess geSource...'
geSourceJob = PreProcessGeSourceJob(
trackName, geSourceManager, allowOverlaps,
self._mode)
anyWarnings = geSourceJob.process()
if self._raiseIfAnyWarnings and anyWarnings and trackName not in self._warningTrackNames:
self._warningTrackNames.append(trackName)
collector.updatePreProcDirtyStatus(
geSourceJob.hasModifiedData())
# Finalize overlapRule output if needed
if anyGeSourceManagers and self._shouldFinalize(
) and collector.preProcIsDirty():
if self._mode == 'Real' and self._shouldMergeChrFolders(
):
self._status = 'Trying to combine chromosome vectors into combined vectors.'
PreProcessUtils.createBoundingRegionShelve(
self._genome, trackName, allowOverlaps)
ChrMemmapFolderMerger.merge(
self._genome, trackName, allowOverlaps)
self._status = 'Trying to remove chromosome folders'
PreProcessUtils.removeChrMemmapFolders(
self._genome, trackName, allowOverlaps)
collector.updatePreProcFilesExistFlag(
allowOverlaps,
preProcFilesExist=True,
merged=True)
self._status = 'Trying to check whether 3D data is correct'
PreProcessUtils.checkIfEdgeIdsExist(
self._genome, trackName, allowOverlaps)
PreProcessUtils.checkUndirectedEdges(
self._genome, trackName, allowOverlaps)
PreProcessUtils.checkUndirectedEdges(
self._genome, trackName, allowOverlaps)
collector.markOverlapRuleAsFinalized(allowOverlaps)
# Finalize track if needed
if self._shouldFinalize():
if collector.preProcIsDirty():
self._status = 'Trying to finalize.'
collector.finalize(self._username,
self._shouldPrintProcessMessages())
if not atLeastOneFinalized:
atLeastOneFinalized = True
else:
collector.removeEntry()
except NotSupportedError, e:
collector.removeEntry()
if DebugConfig.PASS_ON_PREPROCESS_EXCEPTIONS:
raise_from(
PreprocessWarning(
self._addContextToExceptionMsg(e, trackName)), e)
else:
self._printExceptionMsg(e, trackName, Error=False)
except Exception, e:
collector.removeEntry()
if DebugConfig.PASS_ON_PREPROCESS_EXCEPTIONS:
raise_from(
PreprocessError(
self._addContextToExceptionMsg(e, trackName)), e)
else:
self._printExceptionMsg(e, trackName, Error=True)