def test_interbase_range_for_brca2_utr_deletion(): # Deletion of the 6th nucleotide of BRCA2-001's 5' UTR brca2_deletion = Variant("13", 32315479, "T", "", grch38) brca2_001 = grch38.transcripts_by_name("BRCA2-001")[0] interbase_range = interbase_range_affected_by_variant_on_transcript( variant=brca2_deletion, transcript=brca2_001) print(interbase_range) eq_(interbase_range, (5, 6))
def test_interbase_range_for_brca2_utr_insertion(): # T>TC insertion after the 6th nucleotide of BRCA2-001's 5' UTR brca2_insertion = Variant("13", 32315479, "T", "TC", ensembl_grch38) brca2_001 = ensembl_grch38.transcripts_by_name("BRCA2-001")[0] interbase_range = interbase_range_affected_by_variant_on_transcript( variant=brca2_insertion, transcript=brca2_001) print(interbase_range) eq_(interbase_range, (6, 6))
def test_interbase_range_for_brca2_utr_substitution(): # rs769125639 is a simple T>A substitution in the 6th nucleotide of # BRCA2-001's 5' UTR brca2_variant_rs769125639 = Variant("13", 32315479, "T", "A", grch38) brca2_001 = grch38.transcripts_by_name("BRCA2-001")[0] interbase_range = interbase_range_affected_by_variant_on_transcript( variant=brca2_variant_rs769125639, transcript=brca2_001) print(interbase_range) eq_(interbase_range, (5, 6))
def test_interbase_range_for_brca2_utr_substitution(): # rs769125639 is a simple T>A substitution in the 6th nucleotide of # BRCA2-001's 5' UTR brca2_variant_rs769125639 = Variant( "13", 32315479, "T", "A", ensembl_grch38) brca2_001 = ensembl_grch38.transcripts_by_name("BRCA2-001")[0] interbase_range = interbase_range_affected_by_variant_on_transcript( variant=brca2_variant_rs769125639, transcript=brca2_001) print(interbase_range) eq_(interbase_range, (5, 6))