def setUp(self):
genomeAnchor = [0, 101]
self.bins = [
GenomeRegion('TestGenome', 'chr21', 0, 50),
GenomeRegion('TestGenome', 'chr21', 50, 101)
]
self.ts = defaultdict(TrackStructureV2)
allSegmentSetNoOverlap = [[[10, 20]],
[[5, 10], [25, 50], [55, 70], [75, 80],
[90, 95]],
[[5, 15], [20, 30], [45, 55], [75, 80]],
[[0, 20], [60, 65], [85, 100]]]
allSegmentSetOverlap = [[[10, 25]],
[[5, 10], [20, 50], [55, 70], [75, 80],
[90, 95]],
[[5, 20], [15, 30], [45, 55], [75, 80]],
[[0, 20], [60, 65], [85, 100]]]
excludedSegments = [[45, 55], [70, 75]]
for allowOverlaps, allSegmentSet in \
zip([False, True], [allSegmentSetNoOverlap, allSegmentSetOverlap]):
for i, segmentSet in enumerate(allSegmentSet):
track = SampleTrack(
SampleTV(segments=segmentSet,
anchor=genomeAnchor,
allowOverlaps=allowOverlaps))
track.getUniqueKey = MagicMock(return_value=i)
self.ts[allowOverlaps]['dummy' + str(i)] = SingleTrackTS(
track, {})
track = SampleTrack(
SampleTV(segments=[],
anchor=genomeAnchor,
allowOverlaps=allowOverlaps))
track.getUniqueKey = MagicMock(return_value=i + 1)
self.ts[allowOverlaps]['emptyTrack'] = SingleTrackTS(track, {})
exclusionTrack = SampleTrack(
SampleTV(segments=excludedSegments,
anchor=genomeAnchor,
allowOverlaps=False))
self.exclusionTs = SingleTrackTS(exclusionTrack, {})
def setUp(self):
"""
Create a fake trackstructure containing empty tracks,
this is only used to ensure the randomization pool knows there should be 3 input tracks.
"""
genomeAnchor = [0, 101]
self.amountTracks = 3
self.region = GenomeRegion('TestGenome', 'chr21', genomeAnchor[0],
genomeAnchor[1])
self.ts = TrackStructureV2()
for i, segmentSet in enumerate([[]] * self.amountTracks):
track = SampleTrack(
SampleTV(segments=segmentSet, anchor=genomeAnchor))
track.getUniqueKey = MagicMock(return_value=i)
self.ts[str(i)] = SingleTrackTS(track, {})
self.shufflePool = ShuffleElementsBetweenTracksPool(
self.ts, self.region, None)