def test_translate_to():
exons = []
for i, pair in enumerate([(5, 10), (20, 30), (50, 80)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '-', None))
t = dict()
t["muid"] = Transcript("muid", "source", "mRNA", "chr1", 5, 80, '-', 0,
exons, exons, None, None, dict())
g = Gene("guid", "source", "chr1", t["muid"].start, t["muid"].end,
t["muid"].strand, t["muid"].score, t, [], dict())
new_start = 1000
assert g.chrom == "chr1"
assert t["muid"].chrom == "chr1"
assert t["muid"].exons[0].chrom == "chr1"
g.translate_to(new_start)
assert g.chrom == "chr1"
assert t["muid"].chrom == "chr1"
assert t["muid"].exons[0].chrom == "chr1"
g.translate_to(new_start, "other")
assert g.chrom == "other"
assert g.start == new_start
assert g.end == 1075
assert t["muid"].start == new_start
assert t["muid"].end == 1075
assert t["muid"].chrom == "other"
assert t["muid"].exons[0].start == 1045
assert t["muid"].exons[0].end == 1075
assert t["muid"].exons[0].chrom == "other"
assert t["muid"].css == 1075
assert t["muid"].ces == 1000
exons = []
for i, pair in enumerate([(5, 10), (20, 30), (50, 80)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '+', None))
t = dict()
t["muid"] = Transcript("muid", "source", "mRNA", "chr1", 5, 80, '+', 0,
exons, exons, None, None, dict())
g = Gene("guid", "source", "chr1", t["muid"].start, t["muid"].end,
t["muid"].strand, t["muid"].score, t, [], dict())
new_start = 1000
g.translate_to(new_start, "other2")
assert g.chrom == "other2"
assert g.start == new_start
assert g.end == 1075
assert t["muid"].start == new_start
assert t["muid"].end == 1075
assert t["muid"].chrom == "other2"
assert t["muid"].exons[0].start == 1000
assert t["muid"].exons[0].end == 1005
assert t["muid"].exons[0].chrom == "other2"
assert t["muid"].css == 1000
assert t["muid"].ces == 1075
def test_merge_exons():
exons = []
for i, pair in enumerate([(5, 10), (12, 30), (50, 80)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '-', None))
t = dict()
t["muid"] = Transcript("muid", "source", "mRNA", "chr1", 5, 80, '-', 0,
exons, exons, None, None, dict())
g = Gene("guid", "source", "chr1", t["muid"].start, t["muid"].end,
t["muid"].strand, t["muid"].score, t, [], dict())
for e, p in zip(t['muid'].exons, reversed([(5, 10), (12, 30), (50, 80)])):
assert (e.start, e.end) == p
assert len(g.mrnas["muid"].exons) == 3
g.mrnas["muid"].merge_exons()
for e, p in zip(g.mrnas['muid'].exons, reversed([(5, 30), (50, 80)])):
assert (e.start, e.end) == p
assert len(g.mrnas["muid"].exons) == 2
exons = []
for i, pair in enumerate([(5, 10), (20, 48), (50, 80)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '+', None))
t = dict()
t["muid"] = Transcript("muid", "source", "mRNA", "chr1", 5, 80, '+', 0,
exons, exons, None, None, dict())
g = Gene("guid", "source", "chr1", t["muid"].start, t["muid"].end,
t["muid"].strand, t["muid"].score, t, [], dict())
assert len(g.mrnas["muid"].exons) == 3
g.mrnas["muid"].merge_exons()
merged_exons = [(5, 10), (20, 80)]
for e, p in zip(g.mrnas['muid'].exons, merged_exons):
assert (e.start, e.end) == p
assert len(g.mrnas["muid"].exons) == 2
exons = []
for i, pair in enumerate([(5, 15), (16, 48), (50, 80), (83, 95)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '+', None))
t = dict()
t["muid"] = Transcript("muid", "source", "mRNA", "chr1", 5, 80, '+', 0,
exons, exons, None, None, dict())
g = Gene("guid", "source", "chr1", t["muid"].start, t["muid"].end,
t["muid"].strand, t["muid"].score, t, [], dict())
assert len(t['muid'].exons) == 4
t['muid'].merge_exons()
assert len(t['muid'].exons) == 1
assert t['muid'].exons[0].start, t['muid'].exons[0].end == (5, 95)
def test_change_id():
exons = []
for i, pair in enumerate([(5, 10), (20, 30), (50, 80)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '-', None))
t = dict()
t["muid"] = Transcript("muid", "source", "mRNA", "chr1", 5, 80, '-', 0,
exons, exons, None, None, {"Parent": ["guid"]})
g = Gene("guid", "source", "chr1", t["muid"].start, t["muid"].end,
t["muid"].strand, t["muid"].score, t, [], dict())
assert g.uid == "guid"
assert g.mrnas["muid"].uid == "muid"
assert len(g.mrnas["muid"].attr["Parent"]) == 1
assert "guid" in g.mrnas["muid"].attr["Parent"]
g.change_id("guid2")
assert g.uid == "guid2"
assert g.mrnas["muid"].uid == "muid"
assert len(g.mrnas["muid"].attr["Parent"]) == 1
assert "guid2" in g.mrnas["muid"].attr["Parent"]
def test_gene_equality():
g = Gene("uid", "source", "chr1", 0, 10, '+', 0, dict(), dict(), dict())
assert g == Gene("uid", "source", "chr1", 0, 10, '+', 0, dict(), dict(),
dict())
assert g != Gene("uid", "source", "chr1", 2, 10, '+', 0, dict(), dict(),
dict())
exons = []
for i, pair in enumerate([(5, 10), (20, 30), (50, 80)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '-', None))
t = dict()
t["muid"] = Transcript("muid", "source", "mRNA", "chr1", 5, 80, '-', 0,
exons, exons, None, None, dict())
assert g != Gene("uid", "source", "chr1", 0, 10, '+', 0, t, dict(), dict())
exons = []
for i, pair in enumerate([(5, 10), (20, 30), (50, 82)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '-', None))
t2 = dict()
t2["muid2"] = Transcript("muid2", "source", "mRNA", "chr1", 5, 82, '-', 0,
exons, exons, None, None, dict())
assert Gene("uid", "source", "chr1", 0, 10, '+', 0, t, dict(),
dict()) != Gene("uid", "source", "chr1", 0, 10, '+', 0, t2,
dict(), dict())
def test_extending_five_prime_end():
exons = []
for i, pair in enumerate([(5, 10), (20, 30), (50, 80)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '-', None))
t = dict()
t["muid"] = Transcript("muid", "source", "mRNA", "chr1", 5, 80, '-', 0,
exons, exons, None, None, dict())
g = Gene("guid", "source", "chr1", t["muid"].start, t["muid"].end,
t["muid"].strand, t["muid"].score, t, [], dict())
assert g.end == 80
assert t["muid"].end == 80
assert exons[0].end == 80
assert t["muid"].css == 80
g.extend_five_prime_end_cds("muid", 3)
assert g.end == 83
assert t["muid"].end == 83
assert exons[0].end == 83
assert t["muid"].css == 83
exons = []
for i, pair in enumerate([(5, 10), (20, 30), (50, 80)]):
exons.append(Exon(f"e{i}", "chr1", pair[0], pair[1], 0, 0, '+', None))
t = dict()
t["muid"] = Transcript("muid", "source", "mRNA", "chr1", 5, 80, '+', 0,
exons, exons, None, None, dict())
g = Gene("guid", "source", "chr1", t["muid"].start, t["muid"].end,
t["muid"].strand, t["muid"].score, t, [], dict())
assert g.start == 5
assert t["muid"].start == 5
assert exons[0].start == 5
assert t["muid"].css == 5
g.extend_five_prime_end_cds("muid", 3)
assert g.start == 2
assert t["muid"].start == 2
assert exons[0].start == 2
assert t["muid"].css == 2
def test_gene_lt():
g = Gene("uid", "source", "chr1", 0, 10, '+', 0, dict(), dict(), dict())
assert g < Gene("uid", "source", "chr1", 10, 20, '+', 0, dict(), dict(),
dict())
def test_gene_hashable():
g = Gene("uid", "source", "chr1", 0, 10, '+', 0, dict(), dict(), dict())
d = dict()
d[g] = "test"
assert d[g] == "test"