def test_intersect_15():
"""
A : -------------- -------
------
B : ----- ----------------
R1: ----- ------- (overlap)
----
R2: -------------- ------- (original)
------
R3: ------- (comp_incl)
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=50, name="test",
strand="."))
genset1.add(
GenCoor(chrom="chr1", start=20, end=40, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=70, end=80, name="test", strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(
GenCoor(chrom="chr1", start=25, end=45, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=65, end=95, name="test", strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 3
res = genset1.intersect(genset2, mode="original")
assert len(res) == 3
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 1
def test_intersect_10():
"""
Two separately overlapping regions
A : ------- --------
B : ----- --------
R1: --- ---- (overlap)
R2: ------- -------- (original)
R3: (comp_incl)
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=10, name="test",
strand="."))
genset1.add(
GenCoor(chrom="chr1", start=26, end=35, name="test", strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(GenCoor(chrom="chr1", start=7, end=15, name="test",
strand="."))
genset2.add(
GenCoor(chrom="chr1", start=30, end=40, name="test", strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 2
res = genset1.intersect(genset2, mode="original")
assert len(res) == 2
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 0
def test_intersect_11():
"""
Many various overlapping (mixed)
A : ------------------ -------- ---------
B : ---- ------- ------ ----------
R1: -- ------- -- ---- --- (overlap)
R2: ------------------ -------- --------- (original)
R3: (comp_incl)
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=3, end=30, name="test",
strand="."))
genset1.add(
GenCoor(chrom="chr1", start=50, end=60, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=70, end=85, name="test", strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(GenCoor(chrom="chr1", start=1, end=5, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=10, end=19, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=27, end=35, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=55, end=75, name="test", strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 5
res = genset1.intersect(genset2, mode="original")
assert len(res) == 3
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 0
def test_intersect_7():
"""
Perfect overlapping
A : ------
B : ------
R : ------
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=10, name="test",
strand="."))
genset1.add(
GenCoor(chrom="chr1", start=500, end=550, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=600, end=650, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=700, end=750, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=725, end=800, name="test", strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(GenCoor(chrom="chr1", start=1, end=10, name="test",
strand="."))
genset2.add(
GenCoor(chrom="chr1", start=500, end=550, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=600, end=650, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=700, end=750, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=725, end=800, name="test", strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 6
res = genset1.intersect(genset2, mode="original")
assert len(res) == 5
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 5
def test_intersect_8():
"""
One overlapping region
A : ------
B : --------
R1: -- (overlap)
R2: ------ (original)
R3: (comp_incl)
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=10, name="test",
strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(GenCoor(chrom="chr1", start=7, end=20, name="test",
strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 1
assert res[0].start == 7
assert res[0].end == 10
res = genset1.intersect(genset2, mode="original")
assert len(res) == 1
assert res[0].start == 1
assert res[0].end == 10
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 0
def test_intersect_4():
"""
No overlapping
A : ------ --------- -------
B : ---- ------ ------
R : none
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=5, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=11, end=20, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=33, end=38, name="test", strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(GenCoor(chrom="chr1", start=7, end=9, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=20, end=25, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=26, end=31, name="test", strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 0
res = genset1.intersect(genset2, mode="original")
assert len(res) == 0
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 0
def test_intersect_1():
"""
Two empty sets
A : none
B : none
R : none
"""
genset1 = GenCoorSet(name="Test_set")
genset2 = GenCoorSet(name="Test_set")
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 0
res = genset1.intersect(genset2, mode="original")
assert len(res) == 0
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 0
def test_intersect_3():
"""
A : none
B : -----
R : none
"""
genset1 = GenCoorSet(name="Test_set")
genset2 = GenCoorSet(name="Test_set")
genset2.add(
GenCoor(chrom="chr1", start=10, end=20, name="test", strand="+"))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 0
res = genset1.intersect(genset2, mode="original")
assert len(res) == 0
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 0
def test_intersect_12():
"""
Different chromosomes
A : chr1 -------
B : chr2 -------
R : none
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=10, name="test",
strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(GenCoor(chrom="chr2", start=1, end=10, name="test",
strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 0
res = genset1.intersect(genset2, mode="original")
assert len(res) == 0
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 0
def test_intersect_5():
"""
End-to-end attach
A : ------ ------
B : ------
R : none
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=5, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=11, end=20, name="test", strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(GenCoor(chrom="chr1", start=5, end=11, name="test",
strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 0
res = genset1.intersect(genset2, mode="original")
assert len(res) == 0
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 0
def test_intersect_6():
"""
No length attach
A : . .
B : . .
R : none
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=2, end=2, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=20, end=20, name="test", strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(GenCoor(chrom="chr1", start=5, end=5, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=20, end=20, name="test", strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 1
res = genset1.intersect(genset2, mode="original")
assert len(res) == 1
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 1
def test_intersect_13():
"""
Completely included overlapping
A : ---------------------------
B : ---- ------ -----------
R1: ---- ------ ------ (overlap)
R2: --------------------------- (original)
R3: (comp_incl)
"""
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=50, name="test",
strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(GenCoor(chrom="chr1", start=1, end=5, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=10, end=19, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=45, end=60, name="test", strand="."))
res = genset1.intersect(genset2, mode="overlap")
assert len(res) == 3
res = genset1.intersect(genset2, mode="original")
assert len(res) == 1
res = genset1.intersect(genset2, mode="complete_included")
assert len(res) == 0