class TestSNPAlleleGenerator():
def setup(self):
DB.drop_database('mykrobe-test')
self.pg = AlleleGenerator(
reference_filepath="src/mykrobe/data/BX571856.1.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def test_panel_generator(self):
pg = AlleleGenerator(
reference_filepath="src/mykrobe/data/BX571856.1.fasta")
assert pg.ref is not None
def test_simple_variant(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT"
]
assert self.pg._calculate_length_delta_from_indels(v, []) == 0
assert v.is_indel is False
def test_simple_variant2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC"
]
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGATC"
]
def test_simple_variant_invalid(self):
with pytest.raises(ValueError) as cm:
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=31,
alternate_bases=["T"])
panel = self.pg.create(v)
def test_simple_variant_start(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"
]
assert panel.alts == [
"TGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_variant_end(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2902618,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTAT"
]
assert panel.alts == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTTT"
]
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=2902616,
alternate_bases=["C"])
panel = self.pg.create(v)
assert panel.refs == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTAT"
]
assert panel.alts == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTCTAT"
]
def test_simple_variant_with_nearby_snp(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2])
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT"
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
v3 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"])
panel = self.pg.create(v, context=[v2, v3])
assert panel.refs == [
'CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT',
'CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT',
'CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT',
'CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT'
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_variant_with_multiple_nearby_snps2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
v3 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"])
v4 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"])
v5 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["A"])
assert sorted(self.pg._split_context([v, v3, v4])) == sorted([[v, v4],
[v, v3]])
assert (self.pg._split_context([v3, v4])) == [[v4], [v3]]
assert (self.pg._split_context([v, v3, v4, v5])) == [[v, v4, v5],
[v, v3, v5]]
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert sorted(panel.refs) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGAAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGAATTCAAATTTCATAACATCACCATGAGTTTGAT"
])
assert sorted(panel.alts) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGATATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGATTTCAAATTTCATAACATCACCATGAGTTTGAT"
])
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
v5 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["G"])
v3 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"])
v4 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert sorted(panel.refs) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCAGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTAGTCAAATTTCATAACATCACCATGAGTTTGAT"
])
assert sorted(panel.alts) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTGTCAAATTTCATAACATCACCATGAGTTTGAT"
])
class TestINDELAlleleGenerator():
def setup(self):
DB.drop_database('mykrobe-test')
self.pg = AlleleGenerator(
reference_filepath=f"{DATA_DIR}/BX571856.1.fasta")
self.pg2 = AlleleGenerator(
reference_filepath=f"{DATA_DIR}/NC_000962.3.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def test_simple_deletion1(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AA",
start=31,
alternate_bases=["A"])
assert v.is_indel
assert v.is_deletion
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert self.pg._calculate_length_delta_from_indels(v, []) == 1
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTG"
]
def test_simple_deletion2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AT",
start=32,
alternate_bases=["A"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert panel.alts == [
"ATTAAAGATAGAAATACACGATGCGAGCAACAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_deletion3(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AT",
start=2902618,
alternate_bases=["T"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "TTTATACTACTGCTCAATTTTTTTACTTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNN" in panel.refs
assert panel.alts == [
"TTTATACTACTGCTCAATTTTTTTACTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
def test_simple_deletion4(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert panel.alts == [
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_insertion1(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["TTTC"])
panel = self.pg.create(v)
# assert_no_overlapping_kmers(panel)### Skip this test for vars in first k bases of ref
assert v.is_indel
assert v.is_insertion
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert panel.alts == ["TTTCGATTAAAGATAGAAATACACGATGCGAGC"]
def test_simple_insertion2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["CTTT"])
panel = self.pg.create(v)
# assert_no_overlapping_kmers(panel)### Skip this test for vars in first k bases of ref
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert panel.alts == ["CTTTGATTAAAGATAGAAATACACGATGCGAGCA"]
def test_simple_insertion3(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["ATTT"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCATTTATCAAATTTCATAACATCACCATGAGTTTG"
]
def test_simple_insertion4(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["AGGGG"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert panel.alts == [
"ATTAAAGATAGAAATACACGATGCGAGCAAGGGGTCAAATTTCATAACATCACCATGAGTTTGA"
]
def test_simple_insertion5(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2902618,
alternate_bases=["ATGC"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "TTTATACTACTGCTCAATTTTTTTACTTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNN" in panel.refs
assert panel.alts == [
"TATACTACTGCTCAATTTTTTTACTTTTATGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
def test_double_insertion(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=4021408,
alternate_bases=["ACGCTGGCGGGCG"])
v1 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AGA",
start=4021406,
alternate_bases=["CGG"])
context = [v1]
assert self.pg2._remove_overlapping_contexts(v, [v1]) == []
panel = self.pg2.create(v, context=context)
assert_no_overlapping_kmers(panel)
assert "ATCTAGCCGCAAGGGCGCGAGCAGACGCAGAATCGCATGATTTGAGCTCAAATCATGCGAT" in panel.refs
assert panel.alts == [
"TCTAGCCGCAAGGGCGCGAGCAGACGCAGACGCTGGCGGGCGATCGCATGATTTGAGCTCAAATCATGCGAT"
]
def test_double_indel_fail(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="CCA",
start=2288851,
alternate_bases=["A"])
v1 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2288850,
alternate_bases=["ACC"])
context = [v1]
panel = self.pg2.create(v, context=context)
assert "GGCGCACACAATGATCGGTGGCAATACCGACCACATCGACCTCATCGACGCCGCGTTGCCG" in panel.refs
assert "GGCGCACACAATGATCGGTGGCAATACCGACCACATCGACCTCATCGACGCCGCGTTGCCG" not in panel.alts
def test_large_insertion(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="CCGCCGGCCCCGCCGTTT",
start=1636155,
alternate_bases=[
"CTGCCGGCCCCGCCGGCGCCGCCCAATCCACCGAAGCCCCTCCCTTCGGTGGGGTCGCTGCCGCCGTCGCCGCCGTCACCGCCCTTGCCGCCGGCCCCGCCGTCGCCGCCGGCTCCGGCGGTGCCGTCGCCGCCCTGGCCGCCGGCCCCGCCGTTTCCG"
])
panel = self.pg2.create(v, context=[])
assert_no_overlapping_kmers(panel)
assert "AGACCTAGCAGGGTGCCGGCGCCGCCCTTGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCAT" in panel.refs
assert panel.alts == [
"GACCTAGCAGGGTGCCGGCGCCGCCCTTGCTGCCGGCCCCGCCGGCGCCGCCCAATCCACCGAAGCCCCTCCCTTCGGTGGGGTCGCTGCCGCCGTCGCCGCCGTCACCGCCCTTGCCGCCGGCCCCGCCGTCGCCGCCGGCTCCGGCGGTGCCGTCGCCGCCCTGGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCGCCATCGCCGATGATGTTTTCC"
]
class TestSNPAlleleGenerator:
def setup(self):
DB.drop_database("mykrobe-test")
self.pg = AlleleGenerator(
reference_filepath=f"{DATA_DIR}/BX571856.1.fasta", kmer=31)
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def test_panel_generator(self):
pg = AlleleGenerator(reference_filepath=f"{DATA_DIR}/BX571856.1.fasta",
kmer=31)
assert pg.ref is not None
def test_simple_snp_variant(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
panel = self.pg.create(v)
assert panel.refs[0][:31] != panel.alts[0][:31]
assert panel.refs[0][-32:] != panel.alts[0][-32:]
assert panel.refs[0][-31:] != panel.alts[0][-31:]
assert_no_overlapping_kmers(panel)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG"
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTG"
]
assert self.pg._calculate_length_delta_from_indels(v, []) == 0
assert v.is_indel is False
def test_simple_variant2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert panel.refs == [
"GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA"
]
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGA"
]
def test_simple_variant_invalid(self):
with pytest.raises(ValueError) as cm:
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=31,
alternate_bases=["T"],
)
panel = self.pg.create(v)
def test_simple_variant_start(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["T"],
)
panel = self.pg.create(v)
# assert_no_overlapping_kmers(panel) ## Will have overlapping kmers only if the SNP is in the i
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG"
]
assert panel.alts == [
"TGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG"
]
def test_simple_variant_end(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2902618,
alternate_bases=["T"],
)
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert panel.refs == [
"TTTATACTACTGCTCAATTTTTTTACTTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
assert panel.alts == [
"TTTATACTACTGCTCAATTTTTTTACTTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=2902616,
alternate_bases=["C"],
)
panel = self.pg.create(v)
assert panel.refs == [
"ATTTTATACTACTGCTCAATTTTTTTACTTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
assert panel.alts == [
"ATTTTATACTACTGCTCAATTTTTTTACTTCTATNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
def test_simple_variant_with_nearby_snp(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert set(panel.refs) == set([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTG",
])
assert set(panel.alts) == set([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTG",
])
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"],
)
panel = self.pg.create(v, context=[v2, v3])
assert_no_overlapping_kmers(panel)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT",
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT",
]
def test_simple_variant_with_multiple_nearby_snps2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"],
)
v4 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"],
)
v5 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["A"],
)
assert sorted(self.pg._split_context([v, v3, v4])) == sorted([[v, v4],
[v, v3]])
assert (self.pg._split_context([v3, v4])) == [[v4], [v3]]
assert (self.pg._split_context([v, v3, v4, v5])) == [[v, v4, v5],
[v, v3, v5]]
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert_no_overlapping_kmers(panel)
assert sorted(panel.refs) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGAAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGAATTCAAATTTCATAACATCACCATGAGTTTG",
])
assert sorted(panel.alts) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGATATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGATTTCAAATTTCATAACATCACCATGAGTTTG",
])
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
v5 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["G"],
)
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"],
)
v4 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"],
)
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert_no_overlapping_kmers(panel)
assert sorted(panel.refs) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCAGTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGAGTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTAGTCAAATTTCATAACATCACCATGAGTTTG",
])
assert sorted(panel.alts) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCTGTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTGTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTGTCAAATTTCATAACATCACCATGAGTTTG",
])
