def getTrackData(self, trackName, genome, chr, allowOverlaps, forceChrFolders=False):
trackData = TrackData()
brShelve = BoundingRegionShelve(genome, trackName, allowOverlaps)
if not forceChrFolders and brShelve.fileExists():
chr = None
dir = createDirPath(trackName, genome, chr, allowOverlaps)
for fn in os.listdir(dir):
fullFn = dir + os.sep + fn
if fn[0] == '.' or os.path.isdir(fullFn):
continue
if isBoundingRegionFileName(fn):
if fullFn not in self._fileDict:
self._fileDict[fullFn] = brShelve
trackData.boundingRegionShelve = self._fileDict[fullFn]
continue
prefix, elementDim, dtypeDim, dtype = parseMemmapFileFn(fn)
assert prefix not in trackData
trackData[prefix] = self._getFile(chr, dir, fullFn, elementDim, dtype, dtypeDim)
return trackData
def _getBoundingRegionShelve(self, trackName):
if trackName in [None, []] or ExternalTrackManager.isVirtualTrack(trackName):
brShelve = None
else:
brShelve = BoundingRegionShelve(self.genome, trackName, allowOverlaps=False)
if not brShelve.fileExists():
raise BoundingRegionsNotAvailableError('Bounding regions not available for track: ' + \
prettyPrintTrackName(trackName))
return brShelve
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 __init__(self, genome, trackName, allowOverlaps=False, *args, **kwArgs):
from gtrackcore_memmap.track.memmap.BoundingRegionShelve import BoundingRegionShelve
brShelve = BoundingRegionShelve(genome, trackName, allowOverlaps)
if brShelve.fileExists():
boundingRegions = list(brShelve.getAllBoundingRegions())
else:
boundingRegions = GenomeInfo.getStdChrRegionList(genome)
TrackGenomeElementSource.__init__(
self,
genome=genome,
trackName=trackName,
boundingRegions=boundingRegions,
globalCoords=True,
allowOverlaps=allowOverlaps,
printWarnings=True,
)
def _setUpShelve(self):
self._brShelve = BoundingRegionShelve('TestGenome',['testBoundingRegionShelve'], allowOverlaps=False)
class TestBoundingRegionShelve(unittest.TestCase):
def setUp(self):
self._path = createDirPath(['testBoundingRegionShelve'], 'TestGenome', allowOverlaps=False)
self._fn = self._path + os.sep + 'boundingRegions.shelve'
def _setUpShelve(self):
self._brShelve = BoundingRegionShelve('TestGenome',['testBoundingRegionShelve'], allowOverlaps=False)
def tearDown(self):
if os.path.exists(self._path):
shutil.rmtree(self._path)
def testNoBoundingRegions(self):
for sparse in [False, True]:
self._setUpShelve()
self._brShelve.storeBoundingRegions([], [], sparse)
self.assertEquals(BoundingRegionInfo(50000, 52000, 0, 0, 0, 0),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chr21', 50000, 52000)))
def _commonStoreBoundingRegions(self, sparse):
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 10 if sparse else 1000000),\
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 2000000, 2500000), 20 if sparse else 500000),\
BoundingRegionTuple(GenomeRegion('TestGenome', 'chrM', 1000, 2000), 5 if sparse else 1000)]
self._brShelve.storeBoundingRegions(brTuples, ['chr21', 'chrM'], sparse)
def testShelveFileExists(self):
self._setUpShelve()
self.assertFalse(self._brShelve.fileExists())
self.assertFalse(os.path.exists(self._fn))
self._commonStoreBoundingRegions(sparse=True)
self.assertTrue(self._brShelve.fileExists())
self.assertTrue(os.path.exists(self._fn))
def testShelveLocking(self):
self._setUpShelve()
BoundingRegionShelve('TestGenome',['testBoundingRegionShelve'], allowOverlaps=False)
self._commonStoreBoundingRegions(sparse=True)
BoundingRegionShelve('TestGenome',['testBoundingRegionShelve'], allowOverlaps=False)
def testBoundingRegionsOverlapping(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 10), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 500000, 2500000), 20)]
self.assertRaises(InvalidFormatError, self._brShelve.storeBoundingRegions, brTuples, ['chr21'], sparse=True)
def testBoundingRegionsNoGaps(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 10), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 1000000, 2500000), 20)]
self.assertRaises(InvalidFormatError, self._brShelve.storeBoundingRegions, brTuples, ['chr21'], sparse=True)
def testBoundingRegionsNotPositive(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 0), 1)]
self.assertRaises(InvalidFormatError, self._brShelve.storeBoundingRegions, brTuples, ['chr21'], sparse=True)
def testBoundingRegionsUnsortedInChr(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 2000000, 2500000), 20),\
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 10)]
self.assertRaises(InvalidFormatError, self._brShelve.storeBoundingRegions, brTuples, ['chr21'], sparse=True)
def testBoundingRegionsChrNotGrouped(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 10), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chrM', 1000, 2000), 5), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 2000000, 2500000), 20)]
self.assertRaises(InvalidFormatError, self._brShelve.storeBoundingRegions, brTuples, ['chr21', 'chrM'], sparse=True)
def testBoundingRegionsChrInUnsortedOrder(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chrM', 1000, 2000), 5), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 10), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 2000000, 2500000), 20)]
self._brShelve.storeBoundingRegions(brTuples, ['chr21', 'chrM'], sparse=True)
def testBoundingRegionsNotBoundingAllChrs(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 10), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 2000000, 2500000), 20)]
self.assertRaises(InvalidFormatError, self._brShelve.storeBoundingRegions, brTuples, ['chr21', 'chrM'], sparse=True)
def testBoundingRegionsIncorrectCountSparse(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 10), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 2000000, 2500000), 20), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chrM', 1000, 2000), 5)]
self.assertRaises(InvalidFormatError, self._brShelve.storeBoundingRegions, brTuples, ['chr21'], sparse=True)
def testBoundingRegionIncorrectCountDense(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 1000000), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 2000000, 2500000), 500000), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chrM', 1000, 2000), 500)]
self.assertRaises(InvalidFormatError, self._brShelve.storeBoundingRegions, brTuples, ['chr21', 'chrM'], sparse=False)
def testStdGetBoundingInfoSparse(self):
self._setUpShelve()
self._commonStoreBoundingRegions(sparse=True)
self.assertEquals(BoundingRegionInfo(0, 1000000, 0, 30, 0, 470),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chr21', 50000, 52000)))
self.assertEquals(BoundingRegionInfo(2000000, 2500000, 0, 30, 0, 470),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chr21', 2050000, 2052000)))
self.assertEquals(BoundingRegionInfo(1000, 2000, 30, 35, 470, 471),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chrM', 1000, 2000)))
def testStdGetBoundingInfoDense(self):
self._setUpShelve()
self._commonStoreBoundingRegions(sparse=False)
self.assertEquals(BoundingRegionInfo(0, 1000000, 0, 1000000, 0, 0),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chr21', 50000, 52000)))
self.assertEquals(BoundingRegionInfo(2000000, 2500000, 1000000, 1500000, 0, 0),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chr21', 2050000, 2052000)))
self.assertEquals(BoundingRegionInfo(1000, 2000, 1500000, 1501000, 0, 0),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chrM', 1000, 2000)))
def testGetBoundingInfoEmptyBoundingRegionSparse(self):
self._setUpShelve()
brTuples = [BoundingRegionTuple(GenomeRegion('TestGenome', 'chrM', 1000, 2000), 0), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 0, 1000000), 10), \
BoundingRegionTuple(GenomeRegion('TestGenome', 'chr21', 2000000, 2500000), 20)]
self._brShelve.storeBoundingRegions(brTuples, ['chr21'], sparse=True)
self.assertEquals(BoundingRegionInfo(0, 1000000, 0, 30, 0, 470),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chr21', 50000, 52000)))
self.assertEquals(BoundingRegionInfo(2000000, 2500000, 0, 30, 0, 470),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chr21', 2050000, 2052000)))
self.assertEquals(BoundingRegionInfo(1000, 2000, 0, 0, 0, 0),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chrM', 1000, 2000)))
def _testGetBoundingInfoOutsideCommon(self, sparse):
self._setUpShelve()
self._commonStoreBoundingRegions(sparse=sparse)
self.assertRaises(OutsideBoundingRegionError, \
self._brShelve.getBoundingRegionInfo, \
GenomeRegion('TestGenome', 'chr21', 50000, 1052000))
self.assertRaises(OutsideBoundingRegionError, \
self._brShelve.getBoundingRegionInfo, \
GenomeRegion('TestGenome', 'chr21', 1000000, 1052000))
self.assertRaises(OutsideBoundingRegionError, \
self._brShelve.getBoundingRegionInfo, \
GenomeRegion('TestGenome', 'chrM', 1500, 3000))
self.assertEquals(BoundingRegionInfo(100000, 110000, 0, 0, 0, 0),
self._brShelve.getBoundingRegionInfo(GenomeRegion('TestGenome', 'chr2', 100000, 110000)))
def testGetBoundingInfoOutsideSparse(self):
self._testGetBoundingInfoOutsideCommon(sparse=True)
def testGetBoundingInfoOutsideDense(self):
self._testGetBoundingInfoOutsideCommon(sparse=False)
def testStdGetTotalElementCountForChrSparse(self):
self._setUpShelve()
self._commonStoreBoundingRegions(sparse=True)
self.assertEquals(30,
self._brShelve.getTotalElementCountForChr('chr21'))
self.assertEquals(5,
self._brShelve.getTotalElementCountForChr('chrM'))
self.assertEquals(0,
self._brShelve.getTotalElementCountForChr('chr1'))
def testStdGetTotalElementCountForChrDense(self):
self._setUpShelve()
self._commonStoreBoundingRegions(sparse=False)
self.assertEquals(1500000,
self._brShelve.getTotalElementCountForChr('chr21'))
self.assertEquals(1000,
self._brShelve.getTotalElementCountForChr('chrM'))
self.assertEquals(0,
self._brShelve.getTotalElementCountForChr('chr1'))
def runTest(self):
pass
