def setUp(self):
self.prevCompBinSize = gtrackcore_memmap.util.CompBinManager.COMP_BIN_SIZE
gtrackcore_memmap.util.CompBinManager.COMP_BIN_SIZE = 100
from gtrackcore_memmap.track.memmap.TrackViewLoader import TrackViewLoader
self.trackViewLoader = TrackViewLoader()
def __init__(self, trackName):
self.trackName = trackName
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
class TestTrackViewLoader(TestCaseWithImprovedAsserts):
def setUp(self):
self.prevCompBinSize = gtrackcore_memmap.util.CompBinManager.COMP_BIN_SIZE
gtrackcore_memmap.util.CompBinManager.COMP_BIN_SIZE = 100
from gtrackcore_memmap.track.memmap.TrackViewLoader import TrackViewLoader
self.trackViewLoader = TrackViewLoader()
def tearDown(self):
gtrackcore_memmap.util.CompBinManager.COMP_BIN_SIZE = self.prevCompBinSize
def _assertTrackViewLoading_Numbers(self, trackData, start, end):
trackView = self.trackViewLoader.loadTrackView(
trackData, GenomeRegion(genome="TestGenome", start=start, end=end), "crop", False
)
self.assertListsOrDicts(trackData["val"][start:end], [el.val() for el in trackView])
self.assertListsOrDicts(trackData["strand"][start:end], [el.strand() for el in trackView])
self.assertListsOrDicts(trackData["id"][start:end], [el.id() for el in trackView])
self.assertListsOrDicts(trackData["edges"][start:end], [el.edges() for el in trackView])
self.assertListsOrDicts(trackData["weights"][start:end], [el.weights() for el in trackView])
self.assertListsOrDicts(trackData["a"][start:end], [el.a() for el in trackView])
self.assertListsOrDicts(trackData["b"][start:end], [el.b() for el in trackView])
def _getTrackData_Numbers(self, size):
id, edges, weights = getRandGraphLists(size, maxNumEdges=10)
return TrackData(
{
"val": list(getRandValList(size)),
"strand": list(getRandStrandList(size)),
"id": list(id),
"edges": list(edges),
"weights": list(weights),
"a": [str(x) for x in xrange(size)],
"b": [str(x) for x in xrange(size, 0, -1)],
}
)
def testLoadTrackView_Numbers(self):
trackData = self._getTrackData_Numbers(900)
self._assertTrackViewLoading_Numbers(trackData, 0, 100)
self._assertTrackViewLoading_Numbers(trackData, 0, 900)
self._assertTrackViewLoading_Numbers(trackData, 300, 700)
self._assertTrackViewLoading_Numbers(trackData, 312, 700)
self._assertTrackViewLoading_Numbers(trackData, 300, 687)
self._assertTrackViewLoading_Numbers(trackData, 312, 687)
self._assertTrackViewLoading_Numbers(trackData, 0, 0)
self._assertTrackViewLoading_Numbers(trackData, 300, 300)
self._assertTrackViewLoading_Numbers(trackData, 400, 300)
trackData = self._getTrackData_Numbers(891)
self._assertTrackViewLoading_Numbers(trackData, 800, 880)
self._assertTrackViewLoading_Numbers(trackData, 800, 891)
self._assertTrackViewLoading_Numbers(trackData, 700, 880)
def _assertTrackViewLoading_Segments(self, trackData, indexList, start, end):
trackView = self.trackViewLoader.loadTrackView(
trackData, GenomeRegion(genome="TestGenome", start=start, end=end), "crop", False
)
i = -1
for i, el in enumerate(trackView):
if i < len(indexList):
index = indexList[i]
else:
self.fail()
self.assertEqual(max(0, trackData["start"][index] - start), el.start())
self.assertEqual(min(end, trackData["end"][index]) - start, el.end())
self.assertAlmostEqual(trackData["val"][index], el.val())
self.assertEqual(trackData["strand"][index], el.strand())
self.assertEqual(trackData["id"][index], el.id())
self.assertListsOrDicts(trackData["edges"][index], el.edges())
self.assertListsOrDicts(trackData["weights"][index], el.weights())
self.assertEqual(trackData["a"][index], el.a())
self.assertEqual(trackData["b"][index], el.b())
self.assertRaises(AttributeError, lambda: el.leftIndex)
self.assertRaises(AttributeError, lambda: el.rightIndex)
self.assertEqual(len(indexList), i + 1)
def testLoadTrackView_Segments(self):
id, edges, weights = getRandGraphLists(4)
trackData = TrackData(
{
"start": [10, 210, 260, 410],
"end": [20, 240, 310, 710],
"val": list(getRandValList(4)),
"strand": list(getRandStrandList(4)),
"id": list(id),
"edges": list(edges),
"weights": list(weights),
"a": ["A", "B", "C", "D"],
"b": ["1.0", "2.0", "3.0", "4.0"],
"leftIndex": [0, 1, 1, 1, 3, 3, 3, 3, 4],
"rightIndex": [1, 1, 3, 3, 4, 4, 4, 4, 4],
}
)
self._assertTrackViewLoading_Segments(trackData, [0], 0, 100)
self._assertTrackViewLoading_Segments(trackData, [1, 2], 200, 300)
self._assertTrackViewLoading_Segments(trackData, [0, 1, 2, 3], 0, 900)
self._assertTrackViewLoading_Segments(trackData, [2, 3], 300, 700)
self._assertTrackViewLoading_Segments(trackData, [3], 310, 700)
self._assertTrackViewLoading_Segments(trackData, [2], 300, 410)
self._assertTrackViewLoading_Segments(trackData, [], 310, 410)
self._assertTrackViewLoading_Segments(trackData, [], 0, 0)
self._assertTrackViewLoading_Segments(trackData, [], 300, 300)
self._assertTrackViewLoading_Segments(trackData, [], 400, 400)
def runTest(self):
self.testLoadTrackView_Numbers()
class Track(object):
IS_MEMOIZABLE = True
def __new__(cls, trackName):
if trackName == [] or trackName is None:
return None
else:
if ExternalTrackManager.isVirtualTrack(trackName):
return VirtualMinimalTrack.__new__(VirtualMinimalTrack)
else:
return object.__new__(cls)
def __init__(self, trackName):
self.trackName = trackName
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
def _getRawTrackView(self, region, borderHandling, allowOverlaps):
trackData = self._trackSource.getTrackData(self.trackName, region.genome, region.chr, allowOverlaps)
return self._trackViewLoader.loadTrackView(trackData, region, borderHandling, allowOverlaps, self.trackName)
def getTrackView(self, region):
allowOverlaps = self._trackFormatReq.allowOverlaps()
borderHandling = self._trackFormatReq.borderHandling()
assert allowOverlaps is not None
assert borderHandling is not None
origTrackView = self._getRawTrackView(region, borderHandling, allowOverlaps)
if self.formatConverters is None:
self.formatConverters = getFormatConverters(origTrackView.trackFormat, self._trackFormatReq)
if self.formatConverters == []:
raise IncompatibleTracksError(
prettyPrintTrackName(self.trackName)
+ " with format: "
+ str(origTrackView.trackFormat)
+ ("(" + origTrackView.trackFormat._val + ")" if origTrackView.trackFormat._val else "")
+ " does not satisfy "
+ str(self._trackFormatReq)
)
if not self.formatConverters[0].canHandle(origTrackView.trackFormat, self._trackFormatReq):
raise IncompatibleTracksError(
getClassName(self.formatConverters[0])
+ " does not support conversion from "
+ str(origTrackView.trackFormat)
+ " to "
+ str(self._trackFormatReq)
)
return self.formatConverters[0].convert(origTrackView)
def addFormatReq(self, requestedTrackFormat):
prevFormatReq = self._trackFormatReq
self._trackFormatReq = TrackFormatReq.merge(self._trackFormatReq, requestedTrackFormat)
if self._trackFormatReq is None:
raise IncompatibleTracksError(
str(prevFormatReq) + " is incompatible with additional " + str(requestedTrackFormat)
)
def setFormatConverter(self, converterClassName):
assert self.formatConverters is None
if converterClassName is not None:
self.formatConverters = [getFormatConverterByName(converterClassName)]
def getUniqueKey(self, genome):
assert self.formatConverters is not None and len(self.formatConverters) == 1, "FC: " + str(
self.formatConverters
)
assert not None in [self._trackFormatReq.allowOverlaps(), self._trackFormatReq.borderHandling()]
if not self._trackId:
self._trackId = TrackInfo(genome, self.trackName).id
return hash(
(
tuple(self.trackName),
self._trackId,
getClassName(self.formatConverters[0]),
self.formatConverters[0].VERSION,
self._trackFormatReq.allowOverlaps(),
self._trackFormatReq.borderHandling(),
)
)
