def get_variant_names(self, gene, mutation, protein_coding_var=True):
ref, start, alt = split_var_name(mutation)
gene = self.get_gene(gene)
if start < 0 or not protein_coding_var:
return self._process_DNA_mutation(gene, ref, start, alt)
elif start > 0:
return self._process_coding_mutation(gene, ref, start, alt)
else:
raise ValueError(
"Variants are defined in 1-based coordinates. You can't have pos 0. "
)
def test_make_variant_panel5(self):
ag = AlleleGenerator("mykatlas/data/NC_000962.3.fasta")
gene = self.gm.get_gene("gyrA")
for var in self.gm.get_variant_names("gyrA", "D94X"):
ref, start, alt = split_var_name(var)
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
for alt in panel.alts:
seq = copy.copy(str(gene.seq))
seq = seq.replace(panel.ref, alt)
assert Seq(seq).translate()[93] != "D"
def test_make_variant_panel4(self):
ag = AlleleGenerator("mykatlas/data/NC_000962.3.fasta")
gene = self.gm.get_gene("katG")
for var in self.gm.get_variant_names("katG", "W90R"):
ref, start, alt = split_var_name(var)
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
for alt in panel.alts:
seq = copy.copy(str(gene.seq.reverse_complement()))
seq = seq.replace(panel.ref, alt)
assert seq != str(gene.seq)
assert Seq(seq).reverse_complement().translate()[89] == "R"
def _create_variant(self, probe_name):
names = []
params = get_params(probe_name)
if params.get("mut"):
names.append("_".join([params.get("gene"), params.get("mut")]))
var_name = probe_name.split('?')[0].split('-')[1]
names.append(var_name)
try:
# If it's a variant panel we can create a variant
ref, start, alt = split_var_name(var_name)
return Variant.create(start=start,
reference_bases=ref,
alternate_bases=[alt],
names=names,
info=params)
except AttributeError:
return None