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 "ATCCTGGAGCCCACCAGCGGAAACACCGGCATTTCGCTGGCGATGGCGGCCCGGTTGAAGGGG" in panel.refs
assert panel.alts == [
"CATCCTGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGGCGGCCCGGTTGAAGGGGTA",
"CCATCGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGGCGGCCCGGTTGAAGGGGTAC",
"ATCCTGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGCCGCCGCCTGGCGGCCCGGTTGAAGGGG",
"ATCGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGCCGCCGCCTGGCGGCCCGGTTGAAGGGG"]
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 "ATCATGCGATTCTGCGTCTGCTCGCGAGGCTCGCGTGGCCGCCGGCGCTGGCGGGCGATCTCG" in panel.refs
panel = self.pg2.create(v, context=[v1, v2])
assert sorted(
panel.alts) == sorted(
[
"ATCATGCGATTCTGCGTCTGCTCGCGAGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCTCG",
"ATCATGCGATTCTGCGTCTGCTCGCGATCTAGCCGCAAGGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCTCG",
"ATCATGCGATTCTGCGTCTGCTCGCGAGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCGCG",
"ATCATGCGATTCTGCGTCTGCTCGCGATCTAGCCGCAAGGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCGCG"])
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 setUp(self):
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file2",
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])
self.call_set = VariantCallSet.create(
sample_id="C00123",
name="C00123",
variant_sets=self.variant_sets)
self.variant_snp = Variant.create(variant_sets=self.variant_sets,
start=0, end=1, reference_bases="A",
alternate_bases=["T"],
reference=self.reference)
self.variant_snp_mult_alts = Variant.create(
variant_sets=self.variant_sets,
start=0,
end=1,
reference_bases="T",
alternate_bases=[
"A",
"C"],
reference=self.reference)
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 self.pg._remove_overlapping_contexts(v, [v2, v3]) == [v2, v3]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"GATTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"GATTAGAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"GATTTAGAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATC"])
def setUp(self):
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file2",
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])
self.call_set = VariantCallSet.create(
sample_id="C00123",
name="C00123",
variant_sets=self.variant_sets)
self.variant_snp = Variant.create(variant_sets=self.variant_sets,
start=0, end=1, reference_bases="A",
alternate_bases=["T"],
reference=self.reference)
self.variant_snp_mult_alts = Variant.create(
variant_sets=self.variant_sets,
start=0,
end=1,
reference_bases="T",
alternate_bases=[
"A",
"C"],
reference=self.reference)
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_add_second_vcf_variant_set(self):
# This VCF only has one Variant which is not in the first VCF
vcf = VCF(f="tests/vcf_tests/test2.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
assert VariantSet.objects().count() == 3
assert VariantCallSet.objects().count() == 2
assert VariantCall.objects().count() == 42
assert Variant.objects().count() == 22
assert len(Variant.objects()[0].variant_sets) == 3
assert len(
Variant.objects.get(
names="UNION_BC_k31_var_147").variant_sets) == 3
def _remove_variant_set(self, variant_set_name):
vs = VariantSet.objects.get(name=variant_set_name,
reference_set=self.reference_set)
for call_set in VariantCallSet.objects(variant_sets=vs):
call_set.variant_sets.remove(vs)
call_set.save()
# Remove calls from callsets that only have this variantset
if len(call_set.variant_sets) < 2:
VariantCall.objects(call_set=call_set).delete()
call_set.delete()
# Remove variants that are ONLY from this variant set
Variant.objects(variant_sets=vs, variant_sets__size=2).delete()
VariantSetMetadata.objects(variant_set=vs).delete()
vs.delete()
def test_add_second_vcf_variant_set(self):
# This VCF only has one Variant which is not in the first VCF
vcf = VCF(f="tests/vcf_tests/test3.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
assert VariantSet.objects().count() == 2
assert VariantCallSet.objects().count() == 1
assert VariantCall.objects().count() == 106
assert Variant.objects().count() == 106
assert Variant.snps().count() == 89
assert Variant.indels().count() == 17
assert Variant.insertions().count() == 8
assert Variant.deletions().count() == 8
assert Variant.ph_snps.count() == 1
def test_add_add_variants_and_calls(self):
vcf = VCF(f="tests/vcf_tests/test.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
assert VariantCall.objects().count() == 21
assert Variant.objects().count() == 21
def test_create_SNP(self):
v1 = Variant.create(variant_sets=self.variant_sets, start=0,
end=1, reference_bases="A",
alternate_bases=["T"],
reference=self.reference)
assert v1.start == 0
assert v1.end == 1
assert v1.alternate_bases == ["T"]
assert v1.length == 0
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 "ATCTAGCCGCAAGGGCGCGAGCAGACGCAGAATCGCATGATTTGAGCTCAAATCATGCGATTC" in panel.refs
assert panel.alts == [
"ATCTAGCCGCAAGGGCGCGAGCAGACGCAGACGCTGGCGGGCGATCGCATGATTTGAGCTCAAATCATGCGATTC"
]
def test_simple_variant_invalid(self):
with assert_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_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 self.pg._remove_overlapping_contexts(v, [v2]) == []
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert sorted(
panel.alts) == sorted(
["CGATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTGATC"])
def test_add_new_vcf_variant_set(self):
vcf = VCF(f="tests/vcf_tests/test.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
# We create a global variant set as well as one for the individual VCF
assert VariantSet.objects().count() == 2
vs = VariantSet.objects()[0]
assert len(Variant.objects()[0].variant_sets) == 2
assert vs.name == "test.vcf"
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 "CGACTAGCCACCATCGCGCATCAGTGCGAGGTCAAAAGCGACCAAAGCGAGCAAGTCGCGGAT" in panel.refs
assert panel.alts == \
["CGACTAGCCACCATCGCGCATCAGTGCGAGATCAAAAGCGACCAAAGCGAGCAAGTCGCGGAT",
"CGACTAGCCACCATCGCGCATCAGTGCGAGATCAAAAGCGACCAAAGCGAGCAAGTCGCCGAT"]
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 "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"
]
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 "TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTAT" in panel.refs
assert panel.alts == [
"ATAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTT"
]
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 "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert panel.alts == [
"CTTTGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"
]
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 "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCATTTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTTTTCAAATTTCATAACATCACCATGAGTTTGAT"])
def test_create_insertion(self):
v1 = Variant.create(variant_sets=self.variant_sets,
start=0, end=1, reference_bases="T",
alternate_bases=["TA"],
reference=self.reference)
assert v1.start == 0
assert v1.end == 1
assert v1.alternate_bases == ["TA"]
assert v1.is_insertion
assert v1.is_deletion is False
assert v1.is_indel
assert v1.length == 1
def test_large_insertion(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=2352065,
alternate_bases=[
"CCTCGCCTGGGCTGGCGAGCAGACGCAAAATCCCCCGCACGCCCGGCGTGTCGGGGGATTTTGCGTCTG"
])
panel = self.pg.create(v)
assert "AGCTCGGCCAGCTCAGTCACGTCGCCGCCGCCTCGCCAGTTGACCGCGCCCGCTCGCGGCTAG" in panel.refs
assert panel.alts == [
"AAGTCGTCGAGCGAGAACGGTAGTTCCGCGGTGAACCGGTCCAGCTCGGCCAGCTCAGTCACGTCGCCGCCGCCTCGCCTGGGCTGGCGAGCAGACGCAAAATCCCCCGCACGCCCGGCGTGTCGGGGGATTTTGCGTCTGCTCGCCAGTTGACCGCGCCCGCTCGCGGCTAGCGGGCCTACGTGACGTCGTCATGAGATCCGATGACCGATGGC"
]
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 "AGACCTAGCAGGGTGCCGGCGCCGCCCTTGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCATCG" in panel.refs
assert panel.alts == [
"GGTTGGATCGCCACCGGCGCCACCGGCGCCGCCCGCGCCACCAGCACCGCCGCTGCCATCTGGGTCCGTCGAGTCGCCGAGGACGCCGGCGCCGCCATTGTCGCCAAATACCGTGAGACCTAGCAGGGTGCCGGCGCCGCCCTTGCTGCCGGCCCCGCCGGCGCCGCCCAATCCACCGAAGCCCCTCCCTTCGGTGGGGTCGCTGCCGCCGTCGCCGCCGTCACCGCCCTTGCCGCCGGCCCCGCCGTCGCCGCCGGCTCCGGCGGTGCCGTCGCCGCCCTGGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCGCCATCGCCGATGATGTTTTCCCCGCCCTTGCCGCCAGCCCCAGCGTTCCCGCCGGCTCCGCCACTGGCGCCGGTGCCGCCGGGTGCAACGGCGTTGGCGCCGTTACCGCCGTTGCCGCCTTT"
]
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 "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert self.pg._calculate_length_delta_from_indels(v, []) == 1
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTGATC"
]
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_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_make_variant_panel5(self):
ag = AlleleGenerator("mykatlas/data/NC_000962.3.fasta")
gene = self.gm.get_gene("gyrA")
for var in self.gm.get_variant_names("gyrA", "D94X"):
ref, start, alt = split_var_name(var)
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
for alt in panel.alts:
seq = copy.copy(str(gene.seq))
seq = seq.replace(panel.ref, alt)
assert Seq(seq).translate()[93] != "D"
def test_large_var1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"CGCGGGAGTAGAACGATCGCCAAGTGGTCGGTCTTGGCTGCCCACTTCATCCCCGGCGCCACCGGCAGGTCTCGCGGTCATCTCGACCAACGGAGGGCCGTCGGTGGTTCGTATCCGGCCAAGAACGGCGAGAACGGTTTGTGCCTCTATGCCAGGGTGAATGTCTCATCTCCCAGGCGGACGGTGATATCCAGTTCTCCGCCAAGAGCGGACACGTATTTGCGCAGTGTGTTGACCTGTGCGGAGCCGATGTCGCCGTTCTCGATGCTGGATACCCGGCTCTGCCGGATGTGCGCCAGCGCAGCCACCTGGACCTGGGTGAGTGACTGAGCCGCGCGCAGCTCCCGGAGCCGGAATGCCCGCACTTCATCGCGCATTCGTGCCTTGTGCCGGTCCACCGCCTCCCGGTTAACGGGACGTACGGCGTCCATGTCCCGTAGTGTCATCGCCATCGTGCCACTTACCCTTTCTTGCGCTTGCGCCTCTTTGGCTTCGTGTCCTCGAACTGTGCGAGATGTTCGGCAAACATCTCATCGGCCGCTTTGATCTTCTCGTCGTACCACTGGGTCCACCGCCCGGCCTTGTTACCGGCGGCCAGCATGATCGCCTGCCGCGCCGGGTCGAAGGCGAACAGAATGCGGACCTCGGACCGCCCTTGTGATCCTGGACGCAGCTCCTTCATGTTCTTGTGGCGCGACCCACGCACCGTGTCCACCAGAGGACAGCCAAGTGCGGGGCCCTCTTCCTCGAGAACCTCGATAGCTGCGAACACCAATTCGTAGGTCTCTCGGTCCAAGCCGTTGAGCCAGGCGGAGATGCGCTCCACATCCGCCGTCCACCCCACAGAGTCGCAGAGTAGCGCGATACGCGATATCACACAAGGGTGATATTCCTCCGGGTAAGAGCAGCGGGCGACGGGGCTACCGTCGAGGAAATGCCGGCAGGCGAGGACGGACTCTGCGCACCCGGGCCGTTGAAACAGTAGCCTGTGCCAGGCCGAGAATTCATCCCCACGTATGAGGCAGTACAGTGCGCCGCCGTGCGCGTTCTCCCATGGAACGTTCACGGGCTCCCGTGGATGACAGGCGTTTCATGAACGCCAGCGCCGCCGCAACCCGACCGAAAGCGGTTGACCCCAAGGAGAGCTGGAAGTCGAGGCCACCACCTTCGCCGCGGAGTTGCTCATGCCCGAGAGCGAGACTCGTCCCGAAATACGCCGGCTCGATTTCGGCAAGTTGCTCGAACTGAAGCGGGAATGGGCGTCGACCCGCTCGACCAGCCCCAGCCGGGTGACCAGCCCCAGCCGGGTGACCAGCCGATGCACCGCGGCGATCCCACCGAAGCCGGTGGCATCGATGTTGGCGCCGACCTCGTAGCGCACCGCGCCCGAACCCAGCATCGGCCTGGGCTGCGCCGCCCAGCGTCCAGCCCGCGCGTGCCGCGCCGCCACCCTGCGCCCTCGGCGTGTGATGTTTCGCCGACTCTGTTCATGGGTTATCTTCTTCACCACAAAGGCCTTTCCTGCTGGGCTGTGTTGAGGTCGCAAACCCAGCCAGGGTAAGGCCTTTGGCCTCTCCTACCCGGCCGACACGCTTACTGAAGGCCTAGTCTAGGCAGGCCATTCAATCTGCGGAATCGAAAAATTCGGTTCCAGCCTGCTCGTTTCCTTTCCGACAGCGATCTGACGTTGCGTAACGTCATTTGTACGGACTCTTTTAGCGGCATTGATTTCAGATGCCAACGCCGTCTGTGCTGTAGCGCCGATTGGCCGAAACTGTAAATTTGTATGATTATTTAAATCTTTGACGAACACGCGCCACAAACGTACTATCTCTTTGGCAAAGTCCACCGGCATCTCATTCAACGGTTTTGTTTGCGCGTGGTCGTCATATGTTGGTAACTGTGTAACCGGCCGCCTATCTTGCGCGTGCATCATATGACTATGAATCGGCCTTCTCCAGTGAAATTGATACAAGATCGATCCGATAAGCGGTACCTTGTACACAGTGCAATTGTAGTAATTCGCGTTTTGTCCTACGCTTGTATTCTGCGTGAAGAATTCA",
start=2266659,
alternate_bases=[
"CACGCGAGTTGTAGATGATCGTTGAGTGGTCTTGCTTGGACTTCCATTTCATCTTTTCGACGCGCCAGGTCTCGCGGTCCTCCGGATCTGCGCCCGGTTTGAGTTGCACATCAAGGGGATACGGCTTGACCGACTCGTAGCCGACATGTAAGTCGGCTAGTTTCCGGCCGGCGCTGGCGAGCTGGTCGAAGCGTTCGCGGGTCTCCGGTGTTGGGATGTGCGGGAGCATCTTCTTGAGGTCAGCGGCGTATTTTGTGCGGTAGGCGGGGTCATGCAGCAGGCCGTAGACGTAGTAGAAGATGTCGTCTTTGGTGACTTGGTCGCCGATCGTGTCGCGGTAGAGCTTGAGGATGACGCCGGTGATGTTGTCGACGCGGCGGTAGCCGTGGTCGTCTACTTCGGCGTTGGTGGTGGACTCGAAATCGAGTTCGCCGTCACGTGGTTCGGTCTTCTCGTAGGTCCAGCGCGGGAAGAATTGACCGTTGCTTGAGCCCCAGAATGCGAGATCGGGGATAGCGTTTAGCATCAGACACGAGAAGGGCTTGTCTGAGCCCATGCCAACCACGTAGTAACCGACATTCCCGTGCTCCGGCGTCGGAAACATCGACGGAAGCTGGTAGGTACAGTTGTTGAGCTGCTGGTTGGGGTCGAGGTAGGCGTGCTCTTTCGTAAATGGTCGGTACGTGCCGAGCCGCATTCCCGCGGGAGCGAATTCGATGCGAATGCCTTGTGCCACTTGCCGCTTGTTGATGCGGTCCCAGCTGAACTTGGCCGAGTCCACGGTAATGAGGGCGTCAACCGGCGGGGTCTTGGCGTCCCTTCCGCGGATCTCGTTGATCCGGTCGACCTCCGAGTTGTAGAAGTCGATCGTGCGTCCGATGTTGGCCTCGAGCGCACCACGTGAAAAGTTGTAACACCACGCATCCCGGCTGGTCTTCAAGCCCGCGGAATAGTTCGCGAAGACACGTGTCACGTCAAGAGCAGCCTTCTTGTCGCCGATAACCGGCCACGCGCTGAACGCGTCGTCGCGTTGGTTGACCCAGTCACCGTGCAAGTTGGGTGTGACTGTCTGCCATTCCACCGTGTCGAGGTAGCCGTCGCCGACGATCCGCAACTTCTCCTCGCGACTCAGGTAATCGCCGATGTCGCGGTAAAGGACATCGCATGGCCCGCTGTGCTTCGGATCCTTGATGCCAAGGAAGATCGCCACCGTGTTGCGACTCCCCCCGCCAAAGACCTTGCCGCCTTCCTGGCGTGAGAGTTCCCCAGCTGTGCGCTGGTTCCCCCGCAGGTTGTACACATATACCGCCGCGTAGTCGTCGGCGAGCGACAACCGCATGCCGTCTGCCGTGTTGCCGTCTATGTACCCACCATTGGAGACGAATCCGACAACACCGTTGTCACCAATGCGGTCGGTCGCCCACCGGAACGCGCGAATATACGAGTCGTACAGGCTGTTCTTCAGCTGCGCCGTCGACCGCTTCGCGTACGTCTGCTCAATCCGCCCGTCCAACGTCGGATACTTCACGTTGGCGTTCAGGTCGTTCGCGCTGCTCTGCCCCACCGAGTACGGCGGATTCCCGATGATCACGCTGATCGGCGTCGCCAGCTGTCGCAAGATCCGAGCGTTGTTGTACGGGAACATGATCGCGTCCATCGAGTCCCCGGCTTCGGAAATCTGGAACGTGTCGGCCAGCGCCATCCCGGGGAACGGCTCATAGGCGTCGGCGTCGGCGGTCTTGCCCGCCAAAGCATGGTAGGTCGACTCGATGTTCACCGCGGCGATGTAGTACGCCAGCAGCATGATCTCGTTGGCGTGCAGCTCTTGCGAGTACTTTCGGGTGAGGTCGGCGGCCGTGATCAGGTCGGACTGCAGCAGCCGGGTAATGAATGTGCCCGTCCCGGCGAAGCCGTCCAGAATATGCACGCCCTCGTCGGTCAGCCCGCGCCCGAAATGCTTGCGCGACACGAAATCAGCCGCCCGCACAATGAAGTCCACGACCTCGACCGGCGTGTACACGATCCCCAGCGCCTCGGCCTGCTTCTTGAAGCCGATGCGGAAGAACTTCTCGTACAGCTCGGCGATCACCTGCTGCTTGCCCTCGGCGCTGGTGACCTCGCCGGCGCGCCGTCGCACCGATTCGTAAAAGCCTTCCAACCGAGCGGTTTCGGCCTCCAGGCCGGCACCCCCGACGGTGTCGACCATCTTCTGCATGGCCCGCGACACCGGGTTGTGCGACGCGAAGTCATGCCCGGCGAACAGCGCGTCGAACACCGGCTTGGTGATCAGGTGCTGCGAGAGCATGCTGATCGCGTCATCGGGGGTGATCGAGTCATTGAGGTTATCGCGCAGCCCGGCCAGGAACTGCTCGAACGCCGCCGCCGCCGTAGCGTCGGCGCCGCCGAGCAGGGCGTGGATACGGGTGGTCAGCGTCGCGGCGATGTCGGCGACATCGGCGGCCCACTGCTCCCAATAGGTCCGGGTGCCAACCTTGTCGACGATGCGCGCGTAGATCGCTTCCTGCCACTGCGACAACGAGAACATCGCCAACTGCTCCGCGACGGCGGGTCCCGCCTCGTCGGAGGTCGGCCCGATGTGACCGCCCAACAGCTTGTCGCTGCCTTCACCGGTCTTCGTCGGCTTCACGTTCAGCGCAATGCTGTTCACCATCGCGTCGAAGCGCTCGTCGTGCGACCGCAACGCGTTGAGGACCTGCCACACCACCTTGAACCGTTTGTTGTCGGCCAACGCGGCAGACGGCTCGACACCCTCGGGCACCGCCACCGGCAAGATGACGTACCCGTAGTCCTTGCCGGGCGACTTGCGCATCACCCGACCGACCGACTGCACCACGTCGACGATGGAATTGCGCGGATTCAGGAACAGCACCGCGTCCAGCGCGGGCACGTCGACCCCTTCGGAGAGGCAGCGGGCGTTGGACAGGATGCGGCATTCATCCTCGGCGACCACGCCTTTGAGCCAGGCCAGCTGTTCGTTGCGGACCAGCGCGTTGAACGTCCCGTCCACGTGGCGCACCG"
])
panel = self.pg.create(v)
assert "TGGTGACGCGGGAGTAGAACGATCGCCAAGTGGTCGGTCTTGGCTGCCCACTTCATCCCCGGCGCCACCGGCAGGTCTCGCGGTCATCTCGACCAACGGAGGGCCGTCGGTGGTTCGTATCCGGCCAAGAACGGCGAGAACGGTTTGTGCCTCTATGCCAGGGTGAATGTCTCATCTCCCAGGCGGACGGTGATATCCAGTTCTCCGCCAAGAGCGGACACGTATTTGCGCAGTGTGTTGACCTGTGCGGAGCCGATGTCGCCGTTCTCGATGCTGGATACCCGGCTCTGCCGGATGTGCGCCAGCGCAGCCACCTGGACCTGGGTGAGTGACTGAGCCGCGCGCAGCTCCCGGAGCCGGAATGCCCGCACTTCATCGCGCATTCGTGCCTTGTGCCGGTCCACCGCCTCCCGGTTAACGGGACGTACGGCGTCCATGTCCCGTAGTGTCATCGCCATCGTGCCACTTACCCTTTCTTGCGCTTGCGCCTCTTTGGCTTCGTGTCCTCGAACTGTGCGAGATGTTCGGCAAACATCTCATCGGCCGCTTTGATCTTCTCGTCGTACCACTGGGTCCACCGCCCGGCCTTGTTACCGGCGGCCAGCATGATCGCCTGCCGCGCCGGGTCGAAGGCGAACAGAATGCGGACCTCGGACCGCCCTTGTGATCCTGGACGCAGCTCCTTCATGTTCTTGTGGCGCGACCCACGCACCGTGTCCACCAGAGGACAGCCAAGTGCGGGGCCCTCTTCCTCGAGAACCTCGATAGCTGCGAACACCAATTCGTAGGTCTCTCGGTCCAAGCCGTTGAGCCAGGCGGAGATGCGCTCCACATCCGCCGTCCACCCCACAGAGTCGCAGAGTAGCGCGATACGCGATATCACACAAGGGTGATATTCCTCCGGGTAAGAGCAGCGGGCGACGGGGCTACCGTCGAGGAAATGCCGGCAGGCGAGGACGGACTCTGCGCACCCGGGCCGTTGAAACAGTAGCCTGTGCCAGGCCGAGAATTCATCCCCACGTATGAGGCAGTACAGTGCGCCGCCGTGCGCGTTCTCCCATGGAACGTTCACGGGCTCCCGTGGATGACAGGCGTTTCATGAACGCCAGCGCCGCCGCAACCCGACCGAAAGCGGTTGACCCCAAGGAGAGCTGGAAGTCGAGGCCACCACCTTCGCCGCGGAGTTGCTCATGCCCGAGAGCGAGACTCGTCCCGAAATACGCCGGCTCGATTTCGGCAAGTTGCTCGAACTGAAGCGGGAATGGGCGTCGACCCGCTCGACCAGCCCCAGCCGGGTGACCAGCCCCAGCCGGGTGACCAGCCGATGCACCGCGGCGATCCCACCGAAGCCGGTGGCATCGATGTTGGCGCCGACCTCGTAGCGCACCGCGCCCGAACCCAGCATCGGCCTGGGCTGCGCCGCCCAGCGTCCAGCCCGCGCGTGCCGCGCCGCCACCCTGCGCCCTCGGCGTGTGATGTTTCGCCGACTCTGTTCATGGGTTATCTTCTTCACCACAAAGGCCTTTCCTGCTGGGCTGTGTTGAGGTCGCAAACCCAGCCAGGGTAAGGCCTTTGGCCTCTCCTACCCGGCCGACACGCTTACTGAAGGCCTAGTCTAGGCAGGCCATTCAATCTGCGGAATCGAAAAATTCGGTTCCAGCCTGCTCGTTTCCTTTCCGACAGCGATCTGACGTTGCGTAACGTCATTTGTACGGACTCTTTTAGCGGCATTGATTTCAGATGCCAACGCCGTCTGTGCTGTAGCGCCGATTGGCCGAAACTGTAAATTTGTATGATTATTTAAATCTTTGACGAACACGCGCCACAAACGTACTATCTCTTTGGCAAAGTCCACCGGCATCTCATTCAACGGTTTTGTTTGCGCGTGGTCGTCATATGTTGGTAACTGTGTAACCGGCCGCCTATCTTGCGCGTGCATCATATGACTATGAATCGGCCTTCTCCAGTGAAATTGATACAAGATCGATCCGATAAGCGGTACCTTGTACACAGTGCAATTGTAGTAATTCGCGTTTTGTCCTACGCTTGTATTCTGCGTGAAGAATTCAAACACG" in panel.refs
assert panel.alts == [
"GACCGCCGAGTGCGGCTGGATTGGATTTCACAAGGATGCCAATATCCGGCGCAACGCCGTCGAGCGACGGACGGTGCTCGACACGGGAGCCCGGCTATTCTGTGTGCCGCGGGCCGACATCCTGGCAGAGCAAGTCGCGGCACGGTATATTGCGTCCCTTGCGGCGATTGCCCGTGCCGCACGATTTCCGGGACCATTCATCTACACGGTTCACCCGAGCAAGATCGTTCGCGTGCTCTAGTCGTTCATCGCTCCGTTAACCGCCGGCGAGGCCGTCGACGATCTTCATGGTCTCGACGCTGACGGTGGTCACCTTCTTGATGAGGTCGACGATGTAGGTGGGATCGTCGTGTTCGTCGCACCAGTCGTTGGGGTCGTTGACGATGCCCGACGCTTTGTCGGTGGTGACGCGGTAGCGCTCGATGATCCAGCCGAGCGCCGAGCGGGAGCGAGCAGGTAGCGCTCGGCCTCGTCGGGAATGCCGGCGATGGTGACACGCGAGTTGTAGATGATCGTTGAGTGGTCTTGCTTGGACTTCCATTTCATCTTTTCGACGCGCCAGGTCTCGCGGTCCTCCGGATCTGCGCCCGGTTTGAGTTGCACATCAAGGGGATACGGCTTGACCGACTCGTAGCCGACATGTAAGTCGGCTAGTTTCCGGCCGGCGCTGGCGAGCTGGTCGAAGCGTTCGCGGGTCTCCGGTGTTGGGATGTGCGGGAGCATCTTCTTGAGGTCAGCGGCGTATTTTGTGCGGTAGGCGGGGTCATGCAGCAGGCCGTAGACGTAGTAGAAGATGTCGTCTTTGGTGACTTGGTCGCCGATCGTGTCGCGGTAGAGCTTGAGGATGACGCCGGTGATGTTGTCGACGCGGCGGTAGCCGTGGTCGTCTACTTCGGCGTTGGTGGTGGACTCGAAATCGAGTTCGCCGTCACGTGGTTCGGTCTTCTCGTAGGTCCAGCGCGGGAAGAATTGACCGTTGCTTGAGCCCCAGAATGCGAGATCGGGGATAGCGTTTAGCATCAGACACGAGAAGGGCTTGTCTGAGCCCATGCCAACCACGTAGTAACCGACATTCCCGTGCTCCGGCGTCGGAAACATCGACGGAAGCTGGTAGGTACAGTTGTTGAGCTGCTGGTTGGGGTCGAGGTAGGCGTGCTCTTTCGTAAATGGTCGGTACGTGCCGAGCCGCATTCCCGCGGGAGCGAATTCGATGCGAATGCCTTGTGCCACTTGCCGCTTGTTGATGCGGTCCCAGCTGAACTTGGCCGAGTCCACGGTAATGAGGGCGTCAACCGGCGGGGTCTTGGCGTCCCTTCCGCGGATCTCGTTGATCCGGTCGACCTCCGAGTTGTAGAAGTCGATCGTGCGTCCGATGTTGGCCTCGAGCGCACCACGTGAAAAGTTGTAACACCACGCATCCCGGCTGGTCTTCAAGCCCGCGGAATAGTTCGCGAAGACACGTGTCACGTCAAGAGCAGCCTTCTTGTCGCCGATAACCGGCCACGCGCTGAACGCGTCGTCGCGTTGGTTGACCCAGTCACCGTGCAAGTTGGGTGTGACTGTCTGCCATTCCACCGTGTCGAGGTAGCCGTCGCCGACGATCCGCAACTTCTCCTCGCGACTCAGGTAATCGCCGATGTCGCGGTAAAGGACATCGCATGGCCCGCTGTGCTTCGGATCCTTGATGCCAAGGAAGATCGCCACCGTGTTGCGACTCCCCCCGCCAAAGACCTTGCCGCCTTCCTGGCGTGAGAGTTCCCCAGCTGTGCGCTGGTTCCCCCGCAGGTTGTACACATATACCGCCGCGTAGTCGTCGGCGAGCGACAACCGCATGCCGTCTGCCGTGTTGCCGTCTATGTACCCACCATTGGAGACGAATCCGACAACACCGTTGTCACCAATGCGGTCGGTCGCCCACCGGAACGCGCGAATATACGAGTCGTACAGGCTGTTCTTCAGCTGCGCCGTCGACCGCTTCGCGTACGTCTGCTCAATCCGCCCGTCCAACGTCGGATACTTCACGTTGGCGTTCAGGTCGTTCGCGCTGCTCTGCCCCACCGAGTACGGCGGATTCCCGATGATCACGCTGATCGGCGTCGCCAGCTGTCGCAAGATCCGAGCGTTGTTGTACGGGAACATGATCGCGTCCATCGAGTCCCCGGCTTCGGAAATCTGGAACGTGTCGGCCAGCGCCATCCCGGGGAACGGCTCATAGGCGTCGGCGTCGGCGGTCTTGCCCGCCAAAGCATGGTAGGTCGACTCGATGTTCACCGCGGCGATGTAGTACGCCAGCAGCATGATCTCGTTGGCGTGCAGCTCTTGCGAGTACTTTCGGGTGAGGTCGGCGGCCGTGATCAGGTCGGACTGCAGCAGCCGGGTAATGAATGTGCCCGTCCCGGCGAAGCCGTCCAGAATATGCACGCCCTCGTCGGTCAGCCCGCGCCCGAAATGCTTGCGCGACACGAAATCAGCCGCCCGCACAATGAAGTCCACGACCTCGACCGGCGTGTACACGATCCCCAGCGCCTCGGCCTGCTTCTTGAAGCCGATGCGGAAGAACTTCTCGTACAGCTCGGCGATCACCTGCTGCTTGCCCTCGGCGCTGGTGACCTCGCCGGCGCGCCGTCGCACCGATTCGTAAAAGCCTTCCAACCGAGCGGTTTCGGCCTCCAGGCCGGCACCCCCGACGGTGTCGACCATCTTCTGCATGGCCCGCGACACCGGGTTGTGCGACGCGAAGTCATGCCCGGCGAACAGCGCGTCGAACACCGGCTTGGTGATCAGGTGCTGCGAGAGCATGCTGATCGCGTCATCGGGGGTGATCGAGTCATTGAGGTTATCGCGCAGCCCGGCCAGGAACTGCTCGAACGCCGCCGCCGCCGTAGCGTCGGCGCCGCCGAGCAGGGCGTGGATACGGGTGGTCAGCGTCGCGGCGATGTCGGCGACATCGGCGGCCCACTGCTCCCAATAGGTCCGGGTGCCAACCTTGTCGACGATGCGCGCGTAGATCGCTTCCTGCCACTGCGACAACGAGAACATCGCCAACTGCTCCGCGACGGCGGGTCCCGCCTCGTCGGAGGTCGGCCCGATGTGACCGCCCAACAGCTTGTCGCTGCCTTCACCGGTCTTCGTCGGCTTCACGTTCAGCGCAATGCTGTTCACCATCGCGTCGAAGCGCTCGTCGTGCGACCGCAACGCGTTGAGGACCTGCCACACCACCTTGAACCGTTTGTTGTCGGCCAACGCGGCAGACGGCTCGACACCCTCGGGCACCGCCACCGGCAAGATGACGTACCCGTAGTCCTTGCCGGGCGACTTGCGCATCACCCGACCGACCGACTGCACCACGTCGACGATGGAATTGCGCGGATTCAGGAACAGCACCGCGTCCAGCGCGGGCACGTCGACCCCTTCGGAGAGGCAGCGGGCGTTGGACAGGATGCGGCATTCATCCTCGGCGACCACGCCTTTGAGCCAGGCCAGCTGTTCGTTGCGGACCAGCGCGTTGAACGTCCCGTCCACGTGGCGCACCGAACACGCCAGGCCCGGGCCGTCGTCAACCAATTCGCGGTATGCCTCAACCACTTTCGGGAACAGCTCGGCAACCTGCTTGGACGTCTTGATGTCCTTGGCGAACGCCACCGCCCGACGCATCGGCGGCTCACCGGCGACAATGCCGGTACCGGACCGCTTGGCCAGGCCATTCCAGCAGCCGACGATCTTGGAGGCGTCGTCGAGCATCAGCTCGCCGGAAACCCCGGAGAGTTCCTGCTGCAACCGGGGCGCGATCACGCCCTGATCGACGGTGAGCACCATCACCTTGTAGTCGGTGAGCAGCCCGCGCTCCACCGCCTCGCCGAACGACAGCCGGTGAAACTCCGGCCCGAACGTCAGCTCGTCGTCCATCGACACCAACTCGGCGGAGTGCTGGTCGGCCCTGTCCTTGATGCTCTCGGTGAAAATCCTTGGCGTGGCGGTCATATACAGCCGCCGGGCCGCCTTCAGATACTGACCGTCGTGCACCCGC"
]
def test_very_large_variant3(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"TCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCAT",
start=1355978,
alternate_bases=[
"TCGTCAACGCCCGGTATCTGAGGATCGGTGTTCACCCAATACAAGTCGCATTCACTGGACCGCCAT"
])
panel = self.pg.create(v)
assert "AAACCTCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCATATCTCG" in panel.refs
assert panel.alts == [
"CAAACCTCGTCAACGCCCGGTATCTGAGGATCGGTGTTCACCCAATACAAGTCGCATTCACTGGACCGCCATATCTCGC"
]
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 "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"CGATTGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCCAAA",
"GATTAAGAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"])
panel = self.pg.create(v, context=[v3, v2])
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"CGATTGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCCAAA",
"GATTAAGAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"])
def setUp(self):
self.variant_snp = Variant.create(start=0, end=1, reference_bases="A",
alternate_bases=["T"])
self.predictor = TBPredictor(variant_calls={},
called_genes={})
