def test_fromBed_oneLineBedReturnsMaskerWithOneInterval(self):
bed = StringIO("chrom\t3\t7")
actual = Masker.from_bed(bed)
expected = Masker(IntervalTree([Interval(3, 7, "chrom")]))
assert actual == expected
def test_fromBed_emptyBedReturnsEmpty(self):
bed = StringIO()
actual = Masker.from_bed(bed)
expected = Masker()
assert actual == expected
def test_recordShouldBeFilteredOut_recordDoesNotOverlapReturnsFalse(self, *mock):
masker = Masker(tree=IntervalTree([Interval(10, 20, "chrom1")]))
record = AlignedSegment()
actual = masker.record_should_be_filtered_out(record)
expected = False
assert actual == expected
def test_recordShouldBeFilteredOut_maskSpannedByRecordReturnsTrue(self, *mock):
masker = Masker(tree=IntervalTree([Interval(10, 20, "chrom1")]))
record = AlignedSegment()
actual = masker.record_should_be_filtered_out(record)
expected = True
assert actual == expected
def test_fromBed_twoLinesBedSameIntervalAndChromosomeReturnsMaskerWithOneInterval(
self
):
bed = StringIO("chrom\t3\t7\nchrom\t3\t7")
actual = Masker.from_bed(bed)
expected = Masker(IntervalTree([Interval(3, 7, "chrom")]))
assert actual == expected
def test_fromBed_twoLinesBedReturnsMaskerWithTwoIntervals(self):
bed = StringIO("chrom\t3\t7\nchrom\t8\t10")
actual = Masker.from_bed(bed)
expected = Masker(
IntervalTree([Interval(3, 7, "chrom"), Interval(8, 10, "chrom")])
)
assert actual == expected
def test_fromBed_twoLinesBedSameIntervalDiffChromosomeReturnsMaskerWithTwoIntervals(
self
):
bed = StringIO("chrom1\t3\t7\nchrom2\t3\t7")
actual = Masker.from_bed(bed)
expected = Masker(
IntervalTree([Interval(3, 7, "chrom1"), Interval(3, 7, "chrom2")])
)
assert actual == expected
def test_equality_twoMaskersNotTheSameReturnsFalse(self):
ivs = [(1, 4), (6, 9)]
m1 = Masker(tree=IntervalTree.from_tuples(ivs))
m2 = Masker()
assert m1 != m2
