def test_TP53_translation_from_cdna():
tp53_001 = grch38.transcripts_by_name("TP53-001")[0]
cdna = tp53_001.coding_sequence
amino_acids, ends_with_stop_codon = translate_cdna(
cdna, first_codon_is_start=True)
assert ends_with_stop_codon
eq_(amino_acids, tp53_001.protein_sequence)
def test_mitochondrial_MTND5_translation_from_cdna():
mtnd5_001 = grch38.transcripts_by_name("MT-ND5-201")[0]
cdna = mtnd5_001.coding_sequence
amino_acids, ends_with_stop_codon = translate_cdna(
cdna, first_codon_is_start=True, mitochondrial=True)
assert ends_with_stop_codon
eq_(amino_acids, mtnd5_001.protein_sequence)
def test_mitochondrial_MTND5_translation_from_cdna():
mtnd5_001 = ensembl_grch38.transcripts_by_name("MT-ND5-201")[0]
cdna = mtnd5_001.coding_sequence
amino_acids, ends_with_stop_codon = translate_cdna(
cdna,
first_codon_is_start=True,
mitochondrial=True)
assert ends_with_stop_codon
eq_(amino_acids, mtnd5_001.protein_sequence)
def test_translate_cdna_no_stop_codon():
eq_(translate_cdna("ATGATG", first_codon_is_start=False), ("MM", False))
def test_translate_cdna_CTG_after_start():
eq_(translate_cdna("CTGCTG", first_codon_is_start=False), ("LL", False))
def test_translate_cdna_alternate_CTG_start():
eq_(translate_cdna("CTGCTG", first_codon_is_start=True), ("ML", False))
def test_translate_cdna_stop_codon():
eq_(translate_cdna("ATGATGTAG", first_codon_is_start=False), ("MM", True))
def test_TP53_translation_from_cdna():
tp53_001 = ensembl_grch38.transcripts_by_name("TP53-001")[0]
cdna = tp53_001.coding_sequence
amino_acids, ends_with_stop_codon = translate_cdna(cdna, first_codon_is_start=True)
assert ends_with_stop_codon
eq_(amino_acids, tp53_001.protein_sequence)
def test_translate_cdna_CTG_after_start():
eq_(translate_cdna("CTGCTG", first_codon_is_start=False), ("LL", False))
def test_translate_cdna_alternate_CTG_start():
eq_(translate_cdna("CTGCTG", first_codon_is_start=True), ("ML", False))
