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_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))
