def setUp(self):
self.prevCompBinSize = gold.util.CompBinManager.COMP_BIN_SIZE
gold.util.CompBinManager.COMP_BIN_SIZE = 100
#self.prevCompBinSize = gold.track.TrackViewLoader.COMP_BIN_SIZE
#gold.track.TrackViewLoader.COMP_BIN_SIZE = 100
from gold.track.TrackViewLoader import TrackViewLoader
self.trackViewLoader = TrackViewLoader()
def __init__(self, trackName, trackTitle=None):
self.trackName = trackName
self.trackTitle = trackTitle
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
def __init__(self, trackName):
self.trackName = trackName
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
def setUp(self):
self.prevCompBinSize = gold.util.CompBinManager.COMP_BIN_SIZE
gold.util.CompBinManager.COMP_BIN_SIZE = 100
#self.prevCompBinSize = gold.track.TrackViewLoader.COMP_BIN_SIZE
#gold.track.TrackViewLoader.COMP_BIN_SIZE = 100
from gold.track.TrackViewLoader import TrackViewLoader
self.trackViewLoader = TrackViewLoader()
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()))
class TestTrackViewLoader(TestCaseWithImprovedAsserts):
def setUp(self):
self.prevCompBinSize = gold.util.CompBinManager.COMP_BIN_SIZE
gold.util.CompBinManager.COMP_BIN_SIZE = 100
#self.prevCompBinSize = gold.track.TrackViewLoader.COMP_BIN_SIZE
#gold.track.TrackViewLoader.COMP_BIN_SIZE = 100
from gold.track.TrackViewLoader import TrackViewLoader
self.trackViewLoader = TrackViewLoader()
def tearDown(self):
gold.util.CompBinManager.COMP_BIN_SIZE = self.prevCompBinSize
#gold.track.TrackViewLoader.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, trackTitle=None):
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, trackTitle=None):
self.trackName = trackName
self.trackTitle = trackTitle
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
self._randIndex = 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):
if not self._trackId:
self._trackId = TrackInfo(genome, self.trackName).id
return hash((tuple(self.trackName),
self._trackId if self._trackId else '',
getClassName(self.formatConverters[0]) if self.formatConverters else '',
self.formatConverters[0].VERSION if self.formatConverters else '',
self._trackFormatReq.allowOverlaps() if self._trackFormatReq.allowOverlaps() else '',
self._trackFormatReq.borderHandling() if self._trackFormatReq.borderHandling() else ''))
def resetTrackSource(self):
self._trackSource = TrackSource()
def setRandIndex(self, randIndex):
pass #used only by TsBasedRandomTrack
class Track(object):
IS_MEMOIZABLE = True
def __new__(cls, trackName, trackTitle=None):
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, trackTitle=None):
self.trackName = trackName
self.trackTitle = trackTitle
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
self._hasBeenRead = False
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)
self._hasBeenRead = True
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))
# TODO: track.formatConverters needs a complete overhaul. It is currently used:
# 1) to link tracks with possible choices for track conversion
# 2) to store the choice of format converter made by the user
# 3) to manage the default choice of format converters [=always the first item in the list]
# 4) to hold the currently selected format converter class until needed by getTrackView
def setFormatConverter(self, converterClassName):
assert( self.formatConverters is None )
if converterClassName is not None:
self.formatConverters = [getFormatConverterByName(converterClassName)]
def hasBeenFlaggedAsRead(self):
return self._hasBeenRead
def getUniqueKey(self, genome):
itemsToBeHashed = [tuple(self.trackName)]
itemsToBeHashed.append(self._getTrackId(genome))
if self._trackFormatReq is not None:
if self._trackFormatReq.allowOverlaps() is not None:
itemsToBeHashed.append(self._trackFormatReq.allowOverlaps())
itemsToBeHashed.append(self._trackFormatReq.borderHandling())
itemsToBeHashed.append(getClassName(self.formatConverters[0]) if self.formatConverters else '')
# TODO: Move away from fixed VERSION, as these in practice are never updated. Also for statistics.
itemsToBeHashed.append(self.formatConverters[0].VERSION if self.formatConverters else '')
from config.DebugConfig import DebugConfig
if DebugConfig.VERBOSE:
from gold.application.LogSetup import logMessage
logMessage('Unique key items for track "{}": '.format(self.trackName) +
', '.join(str(_) for _ in itemsToBeHashed))
return hash(tuple(itemsToBeHashed))
def _getTrackId(self, genome):
if not self._trackId:
trackInfo = TrackInfo(genome, self.trackName)
self._trackId = trackInfo.id
return self._trackId if self._trackId else ''
def resetTrackSource(self):
self._trackSource = TrackSource()
class TestTrackViewLoader(TestCaseWithImprovedAsserts):
def setUp(self):
self.prevCompBinSize = gold.util.CompBinManager.COMP_BIN_SIZE
gold.util.CompBinManager.COMP_BIN_SIZE = 100
#self.prevCompBinSize = gold.track.TrackViewLoader.COMP_BIN_SIZE
#gold.track.TrackViewLoader.COMP_BIN_SIZE = 100
from gold.track.TrackViewLoader import TrackViewLoader
self.trackViewLoader = TrackViewLoader()
def tearDown(self):
gold.util.CompBinManager.COMP_BIN_SIZE = self.prevCompBinSize
#gold.track.TrackViewLoader.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()