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 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_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 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_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_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_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_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_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_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_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="CCGCCGGCCCCGCCGTTT", start=1636155, alternate_bases=[ "CTGCCGGCCCCGCCGGCGCCGCCCAATCCACCGAAGCCCCTCCCTTCGGTGGGGTCGCTGCCGCCGTCGCCGCCGTCACCGCCCTTGCCGCCGGCCCCGCCGTCGCCGCCGGCTCCGGCGGTGCCGTCGCCGCCCTGGCCGCCGGCCCCGCCGTTTCCG" ]) panel = self.pg2.create(v, context=[]) assert "AGACCTAGCAGGGTGCCGGCGCCGCCCTTGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCATCG" in panel.refs assert panel.alts == [ "GGTTGGATCGCCACCGGCGCCACCGGCGCCGCCCGCGCCACCAGCACCGCCGCTGCCATCTGGGTCCGTCGAGTCGCCGAGGACGCCGGCGCCGCCATTGTCGCCAAATACCGTGAGACCTAGCAGGGTGCCGGCGCCGCCCTTGCTGCCGGCCCCGCCGGCGCCGCCCAATCCACCGAAGCCCCTCCCTTCGGTGGGGTCGCTGCCGCCGTCGCCGCCGTCACCGCCCTTGCCGCCGGCCCCGCCGTCGCCGCCGGCTCCGGCGGTGCCGTCGCCGCCCTGGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCGCCATCGCCGATGATGTTTTCCCCGCCCTTGCCGCCAGCCCCAGCGTTCCCGCCGGCTCCGCCACTGGCGCCGGTGCCGCCGGGTGCAACGGCGTTGGCGCCGTTACCGCCGTTGCCGCCTTT" ]
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_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_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_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 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_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_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_make_variant_panel4(self): ag = AlleleGenerator("mykatlas/data/NC_000962.3.fasta") gene = self.gm.get_gene("katG") for var in self.gm.get_variant_names("katG", "W90R"): 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.reverse_complement())) seq = seq.replace(panel.ref, alt) assert seq != str(gene.seq) assert Seq(seq).reverse_complement().translate()[89] == "R"
def _create_variant(self, probe_name): names = [] params = get_params(probe_name) if params.get("mut"): names.append("_".join([params.get("gene"), params.get("mut")])) var_name = probe_name.split('?')[0].split('-')[1] names.append(var_name) try: # If it's a variant panel we can create a variant ref, start, alt = split_var_name(var_name) return Variant.create(start=start, reference_bases=ref, alternate_bases=[alt], names=names, info=params) except AttributeError: return None
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={})