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 TestINDELandSNPSAlleleGenerator():
def setup(self):
DB.drop_database('mykrobe-test')
self.pg = AlleleGenerator(
reference_filepath="src/mykrobe/data/BX571856.1.fasta")
self.pg2 = AlleleGenerator(
reference_filepath="src/mykrobe/data/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 teardown(self):
DB.drop_database('mykrobe-test')
def test_ins_with_SNP_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["ATTT"])
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) ### This test seems to fail sometimes, and pass othertimes...
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"GATTAAAGATAGAAATACACGATGCGAGCATTTATCAAATTTCATAACATCACCATGAGTTTG",
"TTAAAGATAGAAATACACGATGCGAGCATTTTTCAAATTTCATAACATCACCATGAGTTTG"])
def test_del_with_SNP_context1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AA",
start=31,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=33,
alternate_bases=["A"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAACAAATTTCATAACATCACCATGAGTTTGA",
"GATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTG"])
def test_del_with_SNP_context2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AA",
start=31,
alternate_bases=["A"])
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 self.pg._remove_overlapping_contexts(v, [v2]) == []
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert sorted(
panel.alts) == sorted(
["GATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTG"])
def test_del_with_ins_context1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AAT",
start=31,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=4,
alternate_bases=["TTTT"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2]) == [v2]
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"GATTAAAGATAGAAATACACGATGCGAGCACAAATTTCATAACATCACCATGAGTTTGAT",
"TTTTAAAGATAGAAATACACGATGCGAGCACAAATTTCATAACATCACCATGAGTTTG"])
def test_del_with_ins_context2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["CTTT"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2]) == [v2]
assert self.pg._remove_contexts_not_within_k(v, [v2]) == []
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
["ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context3(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TT"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2]) == [v2]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"TTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context4(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TT"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TG"])
panel = self.pg.create(v, context=[v2, v3])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2, v3]) == [v2, v3]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"TTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"TTGAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context5(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TT"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=6,
alternate_bases=["AG"])
panel = self.pg.create(v, context=[v2, v3])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2, v3]) == [v2, v3]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"TTAGAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGA",
"TTAGAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"TTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context_where_base_is_deleted1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=33,
alternate_bases=["C"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2]) == []
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
["ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context_where_base_is_deleted2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="TAAA",
start=5,
alternate_bases=["T"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=7,
alternate_bases=["AG"])
panel = self.pg.create(v, context=[v2, v3])
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATC",
"TTAAGAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
panel = self.pg.create(v, context=[v3, v2])
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATC",
"TTAAGAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_snp_with_replace_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="G",
start=2338961,
alternate_bases=["A"])
v1 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="GGATG",
start=2338990,
alternate_bases=["CGATA"])
panel = self.pg2.create(v, context=[v1])
assert_no_overlapping_kmers(panel)
assert "CGACTAGCCACCATCGCGCATCAGTGCGAGGTCAAAAGCGACCAAAGCGAGCAAGTCGCGG" in panel.refs
assert set(panel.alts) == \
set(["CGACTAGCCACCATCGCGCATCAGTGCGAGATCAAAAGCGACCAAAGCGAGCAAGTCGCCG",
"CGACTAGCCACCATCGCGCATCAGTGCGAGATCAAAAGCGACCAAAGCGAGCAAGTCGCGG"])
def test_indel_snp_indel_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="TCGCGTGGC",
start=4021459,
alternate_bases=["GCGAGCAGA"])
v1 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=4021455,
alternate_bases=["ATCTAGCCGCAAG"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=4021489,
alternate_bases=["G"])
panel = self.pg2.create(v) # , context = [v1, v2])
assert_no_overlapping_kmers(panel)
assert "ATCATGCGATTCTGCGTCTGCTCGCGAGGCTCGCGTGGCCGCCGGCGCTGGCGGGCGATCT" in panel.refs
panel = self.pg2.create(v, context=[v1, v2])
assert_no_overlapping_kmers(panel)
assert sorted(
panel.alts) == sorted(
[
"ATCATGCGATTCTGCGTCTGCTCGCGAGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCG",
"ATCATGCGATTCTGCGTCTGCTCGCGAGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCT",
"TGCGTCTGCTCGCGATCTAGCCGCAAGGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCG",
"TGCGTCTGCTCGCGATCTAGCCGCAAGGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCT"])
def test_complex_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATTT",
start=1503643,
alternate_bases=["A"])
v1 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="CCT",
start=1503615,
alternate_bases=["C"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=1503655,
alternate_bases=["ATGCCGCCGCC"])
panel = self.pg2.create(v, context=[v1, v2])
assert_no_overlapping_kmers(panel)
assert "ATCCTGGAGCCCACCAGCGGAAACACCGGCATTTCGCTGGCGATGGCGGCCCGGTTGAAGG" in panel.refs
assert set(panel.alts) == set([
"CCATCGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGGCGGCCCGGTTGAAGGGGT",
"TCCTGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGGCGGCCCGGTTGAAGGGG",
"ATCGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGCCGCCGCCTGGCGGCCCGG",
"TCCTGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGCCGCCGCCTGGCGGCCCGG",
])