def _createTrackCommon(cls, genome, inTrackName, outTrackName, windowSize,
func, username, chrList):
regionList = [
GenomeRegion(genome, chr, 0, GenomeInfo.getChrLen(genome, chr))
for chr in chrList
]
for region in regionList:
PreProcessCustomTrackJob(genome,
outTrackName, [region],
cls._getGeSourceForRegion,
username=username,
preProcess=True,
finalize=False,
inTrackName=inTrackName,
windowSize=windowSize,
func=func).process()
PreProcessCustomTrackJob(genome,
outTrackName,
regionList,
cls._getGeSourceForRegion,
username=username,
preProcess=False,
finalize=True,
inTrackName=inTrackName,
windowSize=windowSize,
func=func).process()
def _compute(self):
if self._kwArgs.get('minimal') == True:
return False
job = PreProcessCustomTrackJob(self._region.genome, self._outTrackName, [self._region], \
self._getGESource, username=self._username, preProcess=True, finalize=False)
job.process()
#To reduce memory consumption
self._children = []
return True
def _combineResults(self):
if False in self._childResults:
return False
assert isIter(self._region)
regionList = list(self._region)
genome = regionList[0].genome
job = PreProcessCustomTrackJob(genome, self._outTrackName, regionList, self._getGESource, \
username=self._username, preProcess=False, finalize=True)
job.process()
return True
def _createNmerTrack(self, nmerList, lowerOrder=None):
nmerLengths = list(set([len(nmer) for nmer in nmerList]))
assert len(nmerLengths) == 1
chainOrder = lowerOrder if lowerOrder is not None else nmerLengths[0]
regionList = GenomeInfo.getStdChrRegionList(self._genome)
for region in regionList:
print '|',
chains = SameValueIndexChainsFactory.load(
self._createPath(chainOrder), region.chr)
for nmer in nmerList:
if len(nmerList) > 1:
print '.',
if lowerOrder is not None:
nmerPrefix = nmer[0:chainOrder]
rawIndexGenerator = chains.getIndexGenerator(
NmerTools.nmerAsInt(nmerPrefix))
indexGenerator = LowerOrderChainWrapper(
rawIndexGenerator, nmerPrefix, nmer, self._genome,
region.chr)
else:
indexGenerator = chains.getIndexGenerator(
NmerTools.nmerAsInt(nmer))
#print 'Length of lower order chain: %i and %i' % (sum(1 for x in indexGenerator), sum(1 for x in indexGenerator))
#print 'Length of wrapped chain: %i and %i' % (sum(1 for x in wrappedIndexGenerator), sum(1 for x in wrappedIndexGenerator))
PreProcessCustomTrackJob(self._genome, self._createTrackName(nmer), [region], \
self._getNmerGeSourceForChr, finalize=False, preProcess=True, \
indexGenerator=indexGenerator).process()
for nmer in nmerList:
try:
PreProcessCustomTrackJob(self._genome, self._createTrackName(nmer), regionList, \
self._getNmerGeSourceForChr, preProcess=False, finalize=True, \
indexGenerator=[0]).process()
except EmptyGESourceError:
PreProcessCustomTrackJob(self._genome, self._createTrackName(nmer), [GenomeRegion(self._genome, regionList[0].chr, -1, 0)], \
self._getNmerGeSourceForChr, preProcess=True, finalize=True, \
indexGenerator=[-1]).process()
return
def _createTrackCommon(cls, genome, inTrackName, outTrackName, windowSize,
func, username, chrList):
regionList = [
GenomeRegion(genome, chr, 0, GenomeInfo.getChrLen(genome, chr))
for chr in chrList
]
PreProcessCustomTrackJob(genome, outTrackName, regionList, cls._getGeSourceForRegion, \
username=username, inTrackName=inTrackName, windowSize=windowSize, func=func).process()
def _preProcessCustomTracks(self,
subTrackName,
regionList,
getGeSourceCallBackFunc,
noOverlapsFileCount=None,
withOverlapsFileCount=None,
noOverlapsChrElCount=None,
withOverlapsChrElCount=None,
**callBackArgs):
trackName = self.TRACK_NAME_PREFIX + subTrackName
for mergeChrFolders in [False, True]:
self._removePreprocessedTrackData(trackName)
print 'mergeChrFolders: {}'.format(mergeChrFolders)
PreProcessCustomTrackJob(self.GENOME,
trackName,
regionList,
getGeSourceCallBackFunc,
username='******',
preProcess=True,
finalize=False,
mergeChrFolders=mergeChrFolders,
**callBackArgs).process()
PreProcessCustomTrackJob(self.GENOME,
trackName,
regionList,
getGeSourceCallBackFunc,
username='******',
preProcess=False,
finalize=True,
mergeChrFolders=mergeChrFolders,
**callBackArgs).process()
if not mergeChrFolders:
if noOverlapsFileCount:
noOverlapsFileCount = (noOverlapsFileCount -
1) * len(regionList)
if withOverlapsFileCount:
withOverlapsFileCount = (withOverlapsFileCount -
1) * len(regionList)
self._assertCounts(trackName, noOverlapsFileCount,
withOverlapsFileCount, noOverlapsChrElCount,
withOverlapsChrElCount)