def test_insertion_mutation():
seq = Seq("AACT")
mutated = mutate.mutate(seq, 1, 'A', 'AG')
assert(len(mutated) == len(seq) + 1)
assert(mutated[0] == seq[0])
assert(mutated[1] == 'A')
assert(mutated[2] == 'G')
assert(mutated[3] == 'C')
def peptide_from_protein_transcript_variant(transcript_id, pos, ref, alt):
"""
Given an ensembl transcript ID, mutate amino acid `ref` to `alt` at
position `pos`.
"""
transcript = _ensembl.get_protein(transcript_id)
if transcript:
try:
return str(mutate(transcript, pos, ref, alt))
except:
logging.warning("Failed to mutate transcript %s (%s)",
transcript_id,
gene_mutation_description(pos, ref, alt))
return None
return None
def peptide_from_protein_transcript_variant(transcript_id, pos, ref, alt):
"""
Given an ensembl transcript ID, mutate amino acid `ref` to `alt` at
position `pos`.
"""
transcript = _ensembl.get_protein(transcript_id)
if transcript:
try:
return str(mutate(transcript, pos, ref, alt))
except:
logging.warning(
"Failed to mutate transcript %s (%s)",
transcript_id,
gene_mutation_description(pos, ref, alt)
)
return None
return None
def test_deletion_mutation():
seq = Seq("AACT")
mutated = mutate.mutate(seq, 1, 'ACT', 'T')
assert(len(mutated) == 2)
assert(mutated[0] == 'A')
assert(mutated[1] == 'T')
def test_snp_mutation():
seq = Seq("AACCTT")
mutated = mutate.mutate(seq, 1, 'A', 'G')
assert(mutated[0] == seq[0])
assert(mutated[1] == 'G')
assert(mutated[2] == seq[2])
