def test_substitution_variant_object(self): test_file_entry = vcf_generator_ver4.FileEntry(test_entry["gene"], test_entry["genomicHgvs"]) test_sub_variant = vcf_generator_ver4.SubstitutionVariant(test_file_entry) self.assertIsNotNone(test_sub_variant) self.assertIsInstance(test_sub_variant, vcf_generator_ver4.SubstitutionVariant) self.assertEqual(test_sub_variant.getPosition(), test_entry["position"]) self.assertEqual(test_sub_variant.getReference(test_sub_variant.getChromosome(), test_entry["position"]), test_entry["ref"]) self.assertEqual(test_sub_variant.getAlteration(), test_entry["alt"])
def test_delins_variant_object(self):
test_delins_entry = {
"gene": "APC",
"genomicHgvs": "g.112174576_112174577delinsAT",
"position": 112174576,
"ref": "GC",
"alt": "AT"
}
test_file_entry = vcf_generator_ver4.FileEntry(test_delins_entry["gene"], test_delins_entry["genomicHgvs"])
test_delins_variant = vcf_generator_ver4.DelinsVariant(test_file_entry)
self.assertIsInstance(test_delins_variant, vcf_generator_ver4.DelinsVariant)
test_non_sub_variant_object(self, test_delins_variant, test_delins_entry)
def test_duplication_variant_object(self):
test_dup_entry = {
"gene": "CFHR5",
"genomicHgvs": "g.196963265dupA",
"position": 196963265,
"ref": "A",
"alt": "AA"
}
test_file_entry = vcf_generator_ver4.FileEntry(test_dup_entry["gene"], test_dup_entry["genomicHgvs"])
test_dup_variant = vcf_generator_ver4.DuplicationVariant(test_file_entry)
self.assertIsInstance(test_dup_variant, vcf_generator_ver4.DuplicationVariant)
test_non_sub_variant_object(self, test_dup_variant, test_dup_entry)
def test_insertion_variant_object(self):
test_ins_entry = {
"gene": "BRCA1",
"genomicHgvs": "g.41244808_41244809insA",
"position": 41244808,
"ref": "C",
"alt": "CA"
}
test_file_entry = vcf_generator_ver4.FileEntry(test_ins_entry["gene"], test_ins_entry["genomicHgvs"])
test_ins_variant = vcf_generator_ver4.InsertionVariant(test_file_entry)
self.assertIsInstance(test_ins_variant, vcf_generator_ver4.InsertionVariant)
test_non_sub_variant_object(self, test_ins_variant, test_ins_entry)
def test_deletion_variant_object(self):
test_del_entry = {
"gene": "BRCA1",
"genomicHgvs": "g.41209107delG",
"position": 41209106,
"ref": "TG",
"alt": "T"
}
test_file_entry = vcf_generator_ver4.FileEntry(test_del_entry["gene"], test_del_entry["genomicHgvs"])
test_del_variant = vcf_generator_ver4.DeletionVariant(test_file_entry)
self.assertIsInstance(test_del_variant, vcf_generator_ver4.DeletionVariant)
test_non_sub_variant_object(self, test_del_variant, test_del_entry)
def test_variant_object(self): test_variant = vcf_generator_ver4.Variant(vcf_generator_ver4.FileEntry(test_entry["gene"], test_entry["genomicHgvs"])) self.assertIsNotNone(test_variant) self.assertIsInstance(test_variant, vcf_generator_ver4.Variant) self.assertEqual(test_variant.getChromosome(), test_entry["chrom"])
def test_file_entry_object(self): test_file_entry = vcf_generator_ver4.FileEntry(test_entry["gene"], test_entry["genomicHgvs"]) self.assertIsNotNone(test_file_entry) self.assertIsInstance(test_file_entry, vcf_generator_ver4.FileEntry) self.assertEqual(test_file_entry.gene, test_entry["gene"]) self.assertEqual(test_file_entry.genomicHgvs, test_entry["genomicHgvs"])
def create_file_objects(test_entries): test_file_objects = list() for test_entry in test_entries: test_file_objects.append(vcf_generator_ver4.FileEntry(test_entry["gene"], test_entry["genomicHgvs"])) return test_file_objects