def test_locus_distance():
locus_chr1_10_20_pos = Locus("1", 10, 20, "+")
locus_chr1_21_25_pos = Locus("1", 21, 25, "+")
locus_chr2_21_25_pos = Locus("2", 21, 25, "+")
locus_chr1_21_25_neg = Locus("1", 21, 25, "-")
assert locus_chr1_10_20_pos.distance_to_locus(locus_chr1_21_25_pos) == 1
assert locus_chr1_21_25_pos.distance_to_locus(locus_chr1_10_20_pos) == 1
inf = float("inf")
assert locus_chr1_10_20_pos.distance_to_locus(locus_chr2_21_25_pos) == inf
assert locus_chr1_10_20_pos.distance_to_locus(locus_chr1_21_25_neg) == inf
def test_locus_distance():
locus_chr1_10_20_pos = Locus("1", 10, 20, "+")
locus_chr1_21_25_pos = Locus("1", 21, 25, "+")
locus_chr2_21_25_pos = Locus("2", 21, 25, "+")
locus_chr1_21_25_neg = Locus("1", 21, 25, "-")
assert locus_chr1_10_20_pos.distance_to_locus(locus_chr1_21_25_pos) == 1
assert locus_chr1_21_25_pos.distance_to_locus(locus_chr1_10_20_pos) == 1
inf = float("inf")
assert locus_chr1_10_20_pos.distance_to_locus(locus_chr2_21_25_pos) == inf
assert locus_chr1_10_20_pos.distance_to_locus(locus_chr1_21_25_neg) == inf
def test_locus_contains():
locus = Locus("1", 10, 20, "+")
assert locus.contains("1", 10, 20, "+")
assert locus.contains("1", 10, 20)
assert locus.contains("1", 15, 16)
assert locus.contains("1", 10, 10)
assert locus.contains("1", 20, 20)
# before start and after end
assert not locus.contains("1", 5, 30)
# before start
assert not locus.contains("1", 1, 9)
assert not locus.contains("1", 5, 15)
# after end
assert not locus.contains("1", 21, 30)
assert not locus.contains("1", 15, 30)
# wrong contig
assert not locus.contains("2", 10, 20)
# wrong strand
assert not locus.contains("1", 10, 20, "-")
def test_position_offset():
forward_locus = Locus("1", 10, 20, "+")
assert forward_locus.offset(10) == 0
assert forward_locus.offset(15) == 5
assert forward_locus.offset(19) == 9
assert forward_locus.offset(20) == 10
negative_locus = Locus("1", 10, 20, "-")
assert negative_locus.offset(10) == 10
assert negative_locus.offset(15) == 5
assert negative_locus.offset(19) == 1
assert negative_locus.offset(20) == 0
# don't allow negative offsets
with assert_raises(ValueError, None):
forward_locus.offset(9)
# don't allow negative offsets
with assert_raises(ValueError, None):
negative_locus.offset(9)
# don't allow offset past the end of the locus
with assert_raises(ValueError, None):
forward_locus.offset(21)
# don't allow offset past the end of the locus
with assert_raises(ValueError, None):
negative_locus.offset(21)
def test_locus_overlaps():
locus = Locus("1", 10, 20, "+")
assert locus.overlaps("1", 10, 20, "+")
assert locus.overlaps("1", 10, 20)
assert locus.overlaps("1", 5, 30)
assert locus.overlaps("1", 15, 16)
assert locus.overlaps("1", 15, 30)
assert locus.overlaps("1", 5, 15)
assert locus.overlaps("1", 10, 10)
assert locus.overlaps("1", 20, 20)
# before start
assert not locus.overlaps(1, 9, 9)
# after end
assert not locus.overlaps(21, 30, 30)
# wrong contig
assert not locus.overlaps("2", 10, 20)
# wrong strand
assert not locus.overlaps("1", 10, 20, "-")
def test_range_offset():
forward_locus = Locus("1", 10, 20, "+")
assert forward_locus.offset_range(10, 20) == (0, 10)
assert forward_locus.offset_range(11, 14) == (1, 4)
assert forward_locus.offset_range(20, 20) == (10, 10)
negative_locus = Locus("1", 10, 20, "-")
assert negative_locus.offset_range(10, 20) == (0, 10)
assert negative_locus.offset_range(11, 14) == (6, 9)
assert negative_locus.offset_range(20, 20) == (0, 0)
# start shouldn't be larger than end
with assert_raises(AssertionError, None):
forward_locus.offset_range(21, 20)
# start shouldn't be larger than end
with assert_raises(AssertionError, None):
negative_locus.offset_range(21, 20)
# don't allow negative offsets
with assert_raises(ValueError, None):
forward_locus.offset_range(9, 10)
# don't allow negative offsets
with assert_raises(ValueError, None):
forward_locus.offset_range(9, 10)
# don't allow negative offsets
with assert_raises(ValueError, None):
negative_locus.offset_range(9, 10)
def test_position_offset():
forward_locus = Locus("1", 10, 20, "+")
assert forward_locus.offset(10) == 0
assert forward_locus.offset(15) == 5
assert forward_locus.offset(19) == 9
assert forward_locus.offset(20) == 10
negative_locus = Locus("1", 10, 20, "-")
assert negative_locus.offset(10) == 10
assert negative_locus.offset(15) == 5
assert negative_locus.offset(19) == 1
assert negative_locus.offset(20) == 0
# don't allow negative offsets
with assert_raises(ValueError):
forward_locus.offset(9)
# don't allow negative offsets
with assert_raises(ValueError):
negative_locus.offset(9)
# don't allow offset past the end of the locus
with assert_raises(ValueError):
forward_locus.offset(21)
# don't allow offset past the end of the locus
with assert_raises(ValueError):
negative_locus.offset(21)
def test_locus_contains():
locus = Locus("1", 10, 20, "+")
assert locus.contains("1", 10, 20, "+")
assert locus.contains("1", 10, 20)
assert locus.contains("1", 15, 16)
assert locus.contains("1", 10, 10)
assert locus.contains("1", 20, 20)
# before start and after end
assert not locus.contains("1", 5, 30)
# before start
assert not locus.contains("1", 1, 9)
assert not locus.contains("1", 5, 15)
# after end
assert not locus.contains("1", 21, 30)
assert not locus.contains("1", 15, 30)
# wrong contig
assert not locus.contains("2", 10, 20)
# wrong strand
assert not locus.contains("1", 10, 20, "-")
def test_locus_overlaps():
locus = Locus("1", 10, 20, "+")
assert locus.overlaps("1", 10, 20, "+")
assert locus.overlaps("1", 10, 20)
assert locus.overlaps("1", 5, 30)
assert locus.overlaps("1", 15, 16)
assert locus.overlaps("1", 15, 30)
assert locus.overlaps("1", 5, 15)
assert locus.overlaps("1", 10, 10)
assert locus.overlaps("1", 20, 20)
# before start
assert not locus.overlaps(1, 9, 9)
# after end
assert not locus.overlaps(21, 30, 30)
# wrong contig
assert not locus.overlaps("2", 10, 20)
# wrong strand
assert not locus.overlaps("1", 10, 20, "-")
def test_range_offset():
forward_locus = Locus("1", 10, 20, "+")
assert forward_locus.offset_range(10, 20) == (0, 10)
assert forward_locus.offset_range(11, 14) == (1, 4)
assert forward_locus.offset_range(20, 20) == (10, 10)
negative_locus = Locus("1", 10, 20, "-")
assert negative_locus.offset_range(10, 20) == (0, 10)
assert negative_locus.offset_range(11, 14) == (6, 9)
assert negative_locus.offset_range(20, 20) == (0, 0)
# start shouldn't be larger than end
with assert_raises(AssertionError):
forward_locus.offset_range(21, 20)
# start shouldn't be larger than end
with assert_raises(AssertionError):
negative_locus.offset_range(21, 20)
# don't allow negative offsets
with assert_raises(ValueError):
forward_locus.offset_range(9, 10)
# don't allow negative offsets
with assert_raises(ValueError):
forward_locus.offset_range(9, 10)
# don't allow negative offsets
with assert_raises(ValueError):
negative_locus.offset_range(9, 10)