def test_make_variant_panel_stop_codon(self):
variants = list(
self.gm.get_variant_names("katG", "W90*", protein_coding_var=True))
assert len(variants) == 3
refs = sorted([split_var_name(v)[0] for v in variants])
alts = sorted([split_var_name(v)[-1] for v in variants])
var = variants[0]
ref, start, alt = split_var_name(var)
assert start == 2155842
assert refs == ["CCA"] * 3
assert alts == sorted(["TTA", "CTA", "TCA"])
def __init__(
self,
var_name,
reference,
gene=None,
mut=None):
self.var_name = var_name
self.gene = gene
if mut:
tmp, self.start, tmp = split_var_name(mut)
self.ref, tmp, self.alt = split_var_name(var_name)
self.standard_table = CodonTable.unambiguous_dna_by_name["Standard"]
self.reference = reference
def __init__(self,
var_name,
reference,
gene=None,
mut=None,
protein_coding_var=False):
self.var_name = var_name
self.gene = gene
if mut:
tmp, self.start, tmp = split_var_name(mut)
self.ref, tmp, self.alt = split_var_name(var_name)
self.standard_table = CodonTable.unambiguous_dna_by_name["Standard"]
self.reference = reference
self.input_mutation_name = mut
self.protein_coding_var = protein_coding_var
def test_make_variant_panel8(self):
ag = AlleleGenerator("src/mykrobe/data/NC_000962.3.fasta")
gene = self.gm.get_gene("eis")
variants = list(
self.gm.get_variant_names("eis", "TG-1T",
protein_coding_var=False))
assert len(variants) == 1
var = variants[0]
ref, start, alt = split_var_name(var)
assert ref == 'CA'
assert start == 2715332
assert alt == 'A'
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
assert len(panel.alts) == 1
alt = panel.alts[0]
# the panel ref/alt seqs go past the end of the gene,
# so can't comparie against gene sequence. Need to get
# subseq from the reference seq
panel_ref_start = self.reference_seq.find(panel.refs[0])
assert panel_ref_start < start < panel_ref_start + len(panel.refs[0])
seq = str(self.reference_seq[panel_ref_start:panel_ref_start +
len(panel.refs[0])])
assert seq == panel.refs[0]
print(alt, seq[:31] + seq[31:])
assert alt == seq[:30] + seq[31:]
DB.drop_database('mykrobe-test')
def test_make_variant_panel6(self):
ag = AlleleGenerator(f"{DATA_DIR}/NC_000962.3.fasta", kmer=31)
gene = self.gm.get_gene("pncA")
variants = list(
self.gm.get_variant_names("pncA",
"CAG28TAA",
protein_coding_var=False))
assert len(variants) == 1
var = variants[0]
ref, start, alt = split_var_name(var)
assert ref == "CTG"
assert start == 2289212
assert alt == "TTA"
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt],
)
panel = ag.create(v)
assert len(panel.alts) == 1
alt = panel.alts[0]
# the panel ref/alt seqs go past the end of the gene,
# so can't comparie against gene sequence. Need to get
# subseq from the reference seq
panel_ref_start = self.reference_seq.find(panel.refs[0])
assert panel_ref_start < start < panel_ref_start + len(panel.refs[0])
seq = str(self.reference_seq[panel_ref_start:panel_ref_start +
len(panel.refs[0])])
assert seq == panel.refs[0]
assert alt == seq[:30] + "TTA" + seq[33:]
DB.drop_database("mykrobe-test")
def variant(self):
ref, start, alt = split_var_name(self.var_name)
return Variant.create(variant_sets=None,
start=int(start),
end=0,
reference_bases=ref,
alternate_bases=[alt],
reference=self.reference)
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("src/mykrobe/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.refs[0], alt)
assert Seq(seq).translate()[93] != "D"
DB.drop_database('mykrobe-test')
def test_make_variant_panel4(self):
ag = AlleleGenerator("src/mykrobe/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.refs[0], alt)
assert seq != str(gene.seq)
assert Seq(seq).reverse_complement().translate()[89] == "R"
DB.drop_database('mykrobe-test')
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
def test_make_variant_panel7(self):
# Test DNA change upstream of a gene on the reverse
# strand. The variant G-10A is in "gene space", ie
# 10 bases upstream of eis is the nucleotide G on the
# reverse strand. That position is 2715342 in the genome,
# and is C on the forwards strand.
# Here's a diagram:
# | <- This C is at -10 in "gene space", so variant G-10A has ref=G
# | ref coord is 2715342, and variant in "ref space" is C2715342T
# CACAGAATCCGACTGTGGCATATGCCGC
# |
# | <- C = last nucleotide of gene, at 2715332
ag = AlleleGenerator(f"{DATA_DIR}/NC_000962.3.fasta", kmer=31)
gene = self.gm.get_gene("eis")
variants = list(
self.gm.get_variant_names("eis", "G-10A",
protein_coding_var=False))
assert len(variants) == 1
var = variants[0]
ref, start, alt = split_var_name(var)
assert ref == "C"
assert start == 2715342
assert alt == "T"
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt],
)
panel = ag.create(v)
assert len(panel.alts) == 1
alt = panel.alts[0]
# the panel ref/alt seqs go past the end of the gene,
# so can't comparie against gene sequence. Need to get
# subseq from the reference seq
panel_ref_start = self.reference_seq.find(panel.refs[0])
assert panel_ref_start < start < panel_ref_start + len(panel.refs[0])
seq = str(self.reference_seq[panel_ref_start:panel_ref_start +
len(panel.refs[0])])
assert seq == panel.refs[0]
assert alt == seq[:30] + "T" + seq[31:]
DB.drop_database("mykrobe-test")
def test_make_variant_panel1(self):
ag = AlleleGenerator(f"{DATA_DIR}/NC_000962.3.fasta")
gene = self.gm.get_gene("rpoB")
for var in self.gm.get_variant_names("rpoB", "D3A"):
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))
assert Seq(seq).translate()[2] == "D"
seq = seq.replace(panel.refs[0][25:], alt[24:])
assert seq != str(gene.seq)
assert Seq(seq).translate()[2] == "A"
DB.drop_database('mykrobe-test')
def test_make_variant_panel2(self):
ag = AlleleGenerator(f"{DATA_DIR}/NC_000962.3.fasta", kmer=31)
gene = self.gm.get_gene("katG")
for var in self.gm.get_variant_names("katG", "E3A"):
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.refs[0][:39],
alt[:39 + len(alt) - len(panel.refs[0])])
assert seq != str(gene.seq)
assert Seq(seq).reverse_complement().translate()[2] == "A"
DB.drop_database("mykrobe-test")
def test_split_name_del(self):
name = "AA12T"
r, pos, a = split_var_name(name)
assert r == "AA"
assert pos == 12
assert a == "T"
def test_split_name3(self):
name = "C-54T"
r, pos, a = split_var_name(name)
assert r == "C"
assert pos == -54
assert a == "T"
def test_split_name2(self):
name = "A12T/A"
r, pos, a = split_var_name(name)
assert r == "A"
assert pos == 12
assert a == "T/A"
