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_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_extend():
genset = GenCoorSet(name="Test_set")
genset.add(GenCoor(chrom="chr1", start=10, end=20, name="test",
strand="+"))
genset.add(GenCoor(chrom="chr1", start=15, end=50, name="test",
strand="-"))
genset.add(
GenCoor(chrom="chr2", start=100, end=200, name="test", strand="."))
ngcs = genset.extend(mode="left", length=5)
assert ngcs.list[0].start == 5
assert ngcs.list[0].end == 20
assert ngcs.list[1].start == 10
assert ngcs.list[1].end == 50
ngcs = genset.extend(mode="right", length=5)
assert ngcs.list[0].start == 10
assert ngcs.list[0].end == 25
assert ngcs.list[1].start == 15
assert ngcs.list[1].end == 55
ngcs = genset.extend(mode="5end", length=5)
assert ngcs.list[0].start == 5
assert ngcs.list[0].end == 20
assert ngcs.list[1].start == 15
assert ngcs.list[1].end == 55
ngcs = genset.extend(mode="3end", length=5)
assert ngcs.list[0].start == 10
assert ngcs.list[0].end == 25
assert ngcs.list[1].start == 10
assert ngcs.list[1].end == 50
ngcs = genset.extend(mode="both", length=5)
assert ngcs.list[0].start == 5
assert ngcs.list[0].end == 25
assert ngcs.list[1].start == 10
assert ngcs.list[1].end == 55
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_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_distance2():
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=5, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=20, end=24, name="test", strand="."))
g = GenCoor(chrom="chr1", start=7, end=19, name="test", strand=".")
res = genset1.distance(g, sign=False)
assert res == 1
def test_total_coverage1():
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=5, name="test", strand="."))
genset1.add(GenCoor(chrom="chr2", start=2, end=4, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr3_random", start=1, end=80, name="test", strand="."))
cov = genset1.total_coverage()
assert cov == 85
def test_GenCoorSet_len():
genset = GenCoorSet(name="Test_set")
genset.add(GenCoor(chrom="chr1", start=10, end=20, name="test",
strand="."))
genset.add(GenCoor(chrom="chr1", start=15, end=50, name="test",
strand="."))
genset.add(
GenCoor(chrom="chr2", start=100, end=200, name="test", strand="."))
assert len(genset) == 3
def test_rm_duplicates2():
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=5, name="test", strand="."))
genset1.add(GenCoor(chrom="chr2", start=2, end=4, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr3_random", start=1, end=80, name="test", strand="."))
genset1.add(GenCoor(chrom="chr2", start=2, end=4, name="test2",
strand="-"))
res = genset1.rm_duplicates(inplace=False)
assert len(res) == 4
def test_standard_chromosome1():
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=50, name="test",
strand="."))
genset1.add(
GenCoor(chrom="chr2", start=20, end=40, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr3_random", start=70, end=80, name="test",
strand="."))
genset1.standard_chromosome()
assert len(genset1) == 2
def test_distances1():
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=5, name="test", strand="."))
genset1.add(
GenCoor(chrom="chr1", start=80, end=84, name="test", strand="."))
genset2 = GenCoorSet(name="Test_set")
genset2.add(
GenCoor(chrom="chr1", start=10, end=15, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=60, end=64, name="test", strand="."))
genset2.add(
GenCoor(chrom="chr1", start=160, end=164, name="test", strand="."))
res = genset1.distances(genset2, sign=False)
print(res)
assert len(res) == 2
assert res == [5, 16]
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_merge():
genset = GenCoorSet(name="Test_set")
genset.add(GenCoor(chrom="chr1", start=10, end=20, name="test",
strand="+"))
genset.add(GenCoor(chrom="chr1", start=15, end=50, name="test",
strand="-"))
genset.add(
GenCoor(chrom="chr2", start=100, end=200, name="test", strand="."))
res = genset.merge(w_return=True)
assert len(res) == 2
assert res[0].start == 10
assert res[0].end == 50
assert res[0].strand == "."
res = genset.merge(w_return=True, strand_specific=True)
assert len(res) == 3
assert res[0].start == 10
assert res[0].end == 20
assert res[0].strand == "+"
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_GenCoor_extract_bed12():
g1 = GenCoor(chrom="chr22",
start=1000,
end=5000,
name="cloneA",
strand="+",
data="1000/t5000/t0/t2/t567, 488/t0, 3512",
score=960)
g1_extracts = g1.extract_bed12()
assert len(g1_extracts) == 2
assert len(g1_extracts[0]) == 567
assert len(g1_extracts[1]) == 488
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_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
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_GenCoor_relocate3():
g1 = GenCoor(chrom="chr1", start=10, end=20, name="test", strand="-")
r = g1.relocate(mode='center as center', inplace=False)
assert r.start == 10
assert r.end == 20
r = g1.relocate(mode='5end as center', inplace=False)
assert r.start == 15
assert r.end == 25
r = g1.relocate(mode='3end as center', inplace=False)
assert r.start == 5
assert r.end == 15
r = g1.relocate(mode='5end as 5end', inplace=False)
assert r.start == 10
assert r.end == 20
r = g1.relocate(mode='3end as 3end', inplace=False)
assert r.start == 10
assert r.end == 20
def test_GenCoor_relocate5():
g1 = GenCoor(chrom="chr1", start=10, end=20, name="test", strand="-")
r = g1.relocate(mode='center as center', width=2, inplace=False)
assert r.start == 14
assert r.end == 16
r = g1.relocate(mode='5end as center', width=2, inplace=False)
assert r.start == 19
assert r.end == 21
r = g1.relocate(mode='3end as center', width=2, inplace=False)
assert r.start == 9
assert r.end == 11
r = g1.relocate(mode='5end as 5end', width=2, inplace=False)
assert r.start == 18
assert r.end == 20
r = g1.relocate(mode='3end as 3end', width=2, inplace=False)
assert r.start == 10
assert r.end == 12
def test_GenCoor_overlap4():
g1 = GenCoor(chrom="chr1", start=1, end=100, name="test", strand=".")
g2 = GenCoor(chrom="chr1", start=99, end=110, name="test", strand=".")
assert g1.overlap(region=g2) is True
def test_total_coverage2():
genset1 = GenCoorSet(name="Test_set")
genset1.add(GenCoor(chrom="chr1", start=1, end=5, name="test", strand="."))
cov = genset1.total_coverage()
assert cov == 4
def test_GenCoor_capital_name():
g1 = GenCoor(chrom="chr1", start=1, end=100, name="capital", strand=".")
g1.capital_name()
assert g1.name == "CAPITAL"
def test_GenCoor_distance5():
g1 = GenCoor(chrom="chr1", start=10, end=65, name="test", strand=".")
g2 = GenCoor(chrom="chr2", start=60, end=70, name="test", strand=".")
assert g2.distance(region=g1, sign=True) == None
def test_GenCoor_distance2():
g1 = GenCoor(chrom="chr1", start=10, end=50, name="test", strand=".")
g2 = GenCoor(chrom="chr1", start=60, end=70, name="test", strand=".")
assert g2.distance(region=g1) == 10
def test_GenCoor_overlap6():
g1 = GenCoor(chrom="chr1", start=1, end=100, name="test", strand="-")
g2 = GenCoor(chrom="chr1", start=99, end=110, name="test", strand="-")
assert g1.overlap(region=g2, strand_specific=True) is True
def test_GenCoor_overlap8():
g1 = GenCoor(chrom="chr1", start=50, end=50, name="test", strand=".")
g2 = GenCoor(chrom="chr1", start=50, end=50, name="test", strand=".")
assert g1.overlap(region=g2) is True