def _createPreProcFiles(self):
geSource = self._geSourceManager.getGESource()
genome = geSource.genome
collector = PreProcMetaDataCollector(genome, self._trackName)
collector.updateMetaDataForFinalization(geSource.getFileSuffix(), geSource.getPrefixList(), \
geSource.getValDataType(), geSource.getValDim(), \
geSource.getEdgeWeightDataType(), geSource.getEdgeWeightDim(), \
geSource.hasUndirectedEdges(),
geSource.getVersion(), PreProcessUtils.constructId(geSource), \
self._geSourceManager.getNumElements(), \
self._geSourceManager.getBoundingRegionTuples(), \
self._geSourceManager.getValCategories(), \
self._geSourceManager.getEdgeWeightCategories(), \
self._allowOverlaps)
if self._geSourceManager.getNumElements() == 0:
return
if self._mode != 'Real':
for ge in geSource:
pass
return
output = OutputManager(genome, self._trackName, self._allowOverlaps, self._geSourceManager)
writeFunc = output.writeRawSlice if geSource.isSliceSource() else output.writeElement
for ge in geSource:
writeFunc(ge)
collector.flagChrsAsPreProcessed(self._allowOverlaps, self._geSourceManager.getAllChrs())
output.close()
def checkUndirectedEdges(genome, trackName, allowOverlaps):
collector = PreProcMetaDataCollector(genome, trackName)
if not (collector.getTrackFormat().isLinked() and collector.hasUndirectedEdges()):
return
complementEdgeWeightDict = {}
for chr in collector.getPreProcessedChrs(allowOverlaps):
trackSource = TrackSource()
trackData = trackSource.getTrackData(trackName, genome, chr, allowOverlaps)
ids = trackData['id']
edges = trackData['edges']
weights = trackData.get('weights')
for i, id in enumerate(ids):
edgesAttr = edges[i][edges[i] != '']
weightsAttr = weights[i][edges[i] != ''] if weights is not None else None
PreProcessUtils._adjustComplementaryEdgeWeightDict(complementEdgeWeightDict, id, edgesAttr, weightsAttr)
if len(complementEdgeWeightDict) != 0:
unmatchedPairs = []
for toId in complementEdgeWeightDict:
for fromId in complementEdgeWeightDict[toId]:
unmatchedPairs.append((fromId, toId, complementEdgeWeightDict[toId][fromId]))
raise InvalidFormatError("Error: All edges are not undirected. The following edges specifications " +\
"are not matched by an opposite edge with equal weight:" + os.linesep +\
os.linesep.join(["from '%s' to '%s'" % (fromId, toId) + \
(" with weight '%s'" % weight if weight != '' else '') \
for fromId, toId, weight in unmatchedPairs]))
def removeOutdatedPreProcessedFiles(genome, trackName, allowOverlaps, mode):
collector = PreProcMetaDataCollector(genome, trackName)
if PreProcessUtils.preProcFilesExist(genome, trackName, allowOverlaps) and not \
collector.hasRemovedPreProcFiles(allowOverlaps):
dirPath = createDirPath(trackName, genome, allowOverlaps=allowOverlaps)
assert dirPath.startswith(Config.PROCESSED_DATA_PATH), \
"Processed data path '%s' does not start with '%s'" % \
(dirPath, Config.PROCESSED_DATA_PATH)
if mode == 'Real':
print 'Removing outdated preprocessed data: ', dirPath
for fn in os.listdir(dirPath):
fullFn = os.path.join(dirPath, fn)
if os.path.isfile(fullFn):
os.unlink(fullFn)
if os.path.isdir(fullFn):
if PreProcessUtils._isOldTypeChromDirectory(fullFn, genome):
shutil.rmtree(fullFn)
else:
print 'Would now have removed outdated preprocessed data if real run: ', dirPath
collector.updateRemovedPreProcFilesFlag(allowOverlaps, True)
if mode == 'Real':
ti = TrackInfo(genome, trackName)
ti.resetTimeOfPreProcessing()
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 _allGESourceManagers(self, trackName, allowOverlaps):
collector = PreProcMetaDataCollector(self._genome, trackName)
if allowOverlaps == False and collector.overlapRuleHasBeenFinalized(True):
for i in range(1):
self._status = 'Trying to prepare preprocessing for track "%s"' % ':'.join(trackName) + \
(' (allowOverlaps: %s)' % allowOverlaps)
yield self._getGESourceManagerFromTrack(trackName)
else:
for geSource in self._allGESources(trackName):
if allowOverlaps == True:
tf = TrackFormat.createInstanceFromGeSource(geSource)
if tf.isDense() or geSource.hasNoOverlappingElements():
return
self._status = 'Trying to prepare preprocessing for track "%s"' % ':'.join(trackName) + \
(' (filename: "%s")' % geSource.getFileName() if geSource.hasOrigFile() else '') + \
(' (allowOverlaps: %s)' % allowOverlaps)
if PreProcessUtils.shouldPreProcessGESource(trackName, geSource, allowOverlaps):
yield self._getGESourceManagerFromGESource(geSource)
def checkIfEdgeIdsExist(genome, trackName, allowOverlaps):
collector = PreProcMetaDataCollector(genome, trackName)
if not collector.getTrackFormat().isLinked():
return
uniqueIds = numpy.array([], dtype='S')
uniqueEdgeIds = numpy.array([], dtype='S')
for chr in collector.getPreProcessedChrs(allowOverlaps):
trackSource = TrackSource()
trackData = trackSource.getTrackData(trackName, genome, chr, allowOverlaps)
uniqueIds = numpy.unique(numpy.concatenate((uniqueIds, trackData['id'][:])))
uniqueEdgeIds = numpy.unique(numpy.concatenate((uniqueEdgeIds, trackData['edges'][:].flatten())))
uniqueIds = uniqueIds[uniqueIds != '']
uniqueEdgeIds = uniqueEdgeIds[uniqueEdgeIds != '']
unmatchedIds = set(uniqueEdgeIds) - set(uniqueIds)
if len(unmatchedIds) > 0:
raise InvalidFormatError("Error: the following ids specified in the 'edges' column do not exist in the dataset: " + ', '.join(sorted(unmatchedIds)))
def merge(genome, trackName, allowOverlaps):
path = createDirPath(trackName, genome, allowOverlaps=allowOverlaps)
collector = PreProcMetaDataCollector(genome, trackName)
chrList = collector.getPreProcessedChrs(allowOverlaps)
if not collector.getTrackFormat().reprIsDense():
chrList = sorted(chrList)
existingChrList = [chr for chr in ChrMemmapFolderMerger._existingChrIter(path, chrList)]
if len(existingChrList) == 0:
raise EmptyGESourceError('No data lines has been read from source file (probably because it is empty).')
firstChrTrackData = TrackSource().getTrackData(trackName, genome, existingChrList[0], allowOverlaps, forceChrFolders=True)
arrayList = firstChrTrackData.keys()
for arrayName in arrayList:
mergedArray = firstChrTrackData[arrayName][:]
elementDim, dtypeDim = parseMemmapFileFn(firstChrTrackData[arrayName].filename)[1:3]
del firstChrTrackData[arrayName]
for chr in existingChrList[1:]:
chrTrackData = TrackSource().getTrackData(trackName, genome, chr, allowOverlaps, forceChrFolders=True)
mergedArray = ChrMemmapFolderMerger.mergeArrays(mergedArray, np.array(chrTrackData[arrayName][:]))
elementDimNew, dtypeDimNew = parseMemmapFileFn(chrTrackData[arrayName].filename)[1:3]
elementDim = max(elementDim, elementDimNew)
dtypeDim = max(dtypeDim, dtypeDimNew)
del chrTrackData[arrayName]
mergedFn = createMemmapFileFn(path, arrayName, elementDim, dtypeDim, str(mergedArray.dtype))
f = np.memmap(mergedFn, dtype=mergedArray.dtype, mode='w+', shape=mergedArray.shape)
f[:] = mergedArray
f.flush()
del f
del mergedArray
def createBoundingRegionShelve(genome, trackName, allowOverlaps):
collector = PreProcMetaDataCollector(genome, trackName)
boundingRegionTuples = collector.getBoundingRegionTuples(allowOverlaps)
if not collector.getTrackFormat().reprIsDense():
boundingRegionTuples = sorted(boundingRegionTuples)
geChrList = collector.getPreProcessedChrs(allowOverlaps)
brShelve = BoundingRegionShelve(genome, trackName, allowOverlaps)
brShelve.storeBoundingRegions(boundingRegionTuples, geChrList, not collector.getTrackFormat().reprIsDense())
#Sanity check
if brShelve.getTotalElementCount() != collector.getNumElements(allowOverlaps):
raise ShouldNotOccurError("Error: The total element count for all bounding regions is not equal to the total number of genome elements. %s != %s" % \
(brShelve.getTotalElementCount(), collector.getNumElements(allowOverlaps)) )
def _findTrackInfoBasedMetaData(self):
if not self._foundTrackInfoBasedMetaData:
if PreProcMetaDataCollector.hasKey(self._genome, self._trackName):
collector = PreProcMetaDataCollector(self._genome, self._trackName)
self._fileSuffix = collector.getFileSuffix()
self._preProcVersion = collector.getPreProcVersion()
self._id = collector.getId()
self._undirectedEdges = True if collector.hasUndirectedEdges() else False
else:
ti = TrackInfo(self._genome, self._trackName)
self._fileSuffix = ti.fileType
self._preProcVersion = ti.preProcVersion
self._id = ti.id
self._undirectedEdges = True if ti.undirectedEdges else False
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)
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 self.PASS_ON_EXCEPTIONS:
raise
else:
self._printExceptionMsg(e, trackName, Error=False)
except Exception, e:
collector.removeEntry()
if self.PASS_ON_EXCEPTIONS:
raise
else:
self._printExceptionMsg(e, trackName, Error=True)