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 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 setup(self):
DB.drop_database("mykrobe-test")
self.pg = AlleleGenerator(
reference_filepath=f"{DATA_DIR}/NC_000962.3.fasta", kmer=31)
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def setup(self):
DB.drop_database('mykrobe-test')
self.pg = AlleleGenerator(
reference_filepath="src/mykrobe/data/BX571856.1.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
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 run(parser, args):
db_name = '%s-%s' % (DB_PREFIX, args.db_name)
DB = connect(db_name, host=args.db_uri)
if args.verbose:
logger.setLevel(level=logging.DEBUG)
else:
logger.setLevel(level=logging.INFO)
al = AlleleGenerator(reference_filepath=args.reference_filepath,
kmer=args.kmer)
_variant_ids = get_non_singelton_variants(db_name)
total = Variant.snps(id__in=_variant_ids).count()
N = 100
pages = math.ceil(total / N)
for page in range(pages):
logger.info("%i of %i - %f%%" %
(page * N, total, round(100 * (page * N) / total, 2)))
for variant in Variant.snps(
id__in=_variant_ids).order_by("start").skip(N * page).limit(N):
# for variant in Variant.snps().order_by("start"):
variant_panel = make_variant_probe(al, variant, args.kmer, DB=DB)
for i, ref in enumerate(variant_panel.refs):
sys.stdout.write(
">ref-%s?var_name=%snum_alts=%i&ref=%s&enum=%i\n" %
(variant_panel.variant.var_hash, variant.var_name[:100],
len(variant_panel.alts),
variant_panel.variant.reference.id, i))
sys.stdout.write("%s\n" % ref)
for i, a in enumerate(variant_panel.alts):
sys.stdout.write(">alt-%s?var_name=%s&enum=%i\n" %
(variant_panel.variant.var_hash,
variant.var_name[:100], i))
sys.stdout.write("%s\n" % a)
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 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")
class TestSNPAlleleGenerator:
def setup(self):
DB.drop_database("mykrobe-test")
self.pg = AlleleGenerator(
reference_filepath=f"{DATA_DIR}/BX571856.1.fasta", kmer=31)
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def test_panel_generator(self):
pg = AlleleGenerator(reference_filepath=f"{DATA_DIR}/BX571856.1.fasta",
kmer=31)
assert pg.ref is not None
def test_simple_snp_variant(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
panel = self.pg.create(v)
assert panel.refs[0][:31] != panel.alts[0][:31]
assert panel.refs[0][-32:] != panel.alts[0][-32:]
assert panel.refs[0][-31:] != panel.alts[0][-31:]
assert_no_overlapping_kmers(panel)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG"
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTG"
]
assert self.pg._calculate_length_delta_from_indels(v, []) == 0
assert v.is_indel is False
def test_simple_variant2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert panel.refs == [
"GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA"
]
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGA"
]
def test_simple_variant_invalid(self):
with pytest.raises(ValueError) as cm:
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=31,
alternate_bases=["T"],
)
panel = self.pg.create(v)
def test_simple_variant_start(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["T"],
)
panel = self.pg.create(v)
# assert_no_overlapping_kmers(panel) ## Will have overlapping kmers only if the SNP is in the i
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG"
]
assert panel.alts == [
"TGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG"
]
def test_simple_variant_end(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2902618,
alternate_bases=["T"],
)
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert panel.refs == [
"TTTATACTACTGCTCAATTTTTTTACTTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
assert panel.alts == [
"TTTATACTACTGCTCAATTTTTTTACTTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=2902616,
alternate_bases=["C"],
)
panel = self.pg.create(v)
assert panel.refs == [
"ATTTTATACTACTGCTCAATTTTTTTACTTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
assert panel.alts == [
"ATTTTATACTACTGCTCAATTTTTTTACTTCTATNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
def test_simple_variant_with_nearby_snp(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert set(panel.refs) == set([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTG",
])
assert set(panel.alts) == set([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTG",
])
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"],
)
panel = self.pg.create(v, context=[v2, v3])
assert_no_overlapping_kmers(panel)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT",
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT",
]
def test_simple_variant_with_multiple_nearby_snps2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"],
)
v4 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"],
)
v5 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["A"],
)
assert sorted(self.pg._split_context([v, v3, v4])) == sorted([[v, v4],
[v, v3]])
assert (self.pg._split_context([v3, v4])) == [[v4], [v3]]
assert (self.pg._split_context([v, v3, v4, v5])) == [[v, v4, v5],
[v, v3, v5]]
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert_no_overlapping_kmers(panel)
assert sorted(panel.refs) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGAAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGAATTCAAATTTCATAACATCACCATGAGTTTG",
])
assert sorted(panel.alts) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGATATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGATTTCAAATTTCATAACATCACCATGAGTTTG",
])
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"],
)
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"],
)
v5 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["G"],
)
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"],
)
v4 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"],
)
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert_no_overlapping_kmers(panel)
assert sorted(panel.refs) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCAGTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGAGTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTAGTCAAATTTCATAACATCACCATGAGTTTG",
])
assert sorted(panel.alts) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGCTGTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGGTGTCAAATTTCATAACATCACCATGAGTTTG",
"CGATTAAAGATAGAAATACACGATGCGAGTTGTCAAATTTCATAACATCACCATGAGTTTG",
])
class TestINDELAlleleGenerator():
def setup(self):
DB.drop_database('mykrobe-test')
self.pg = AlleleGenerator(
reference_filepath=f"{DATA_DIR}/BX571856.1.fasta")
self.pg2 = AlleleGenerator(
reference_filepath=f"{DATA_DIR}/NC_000962.3.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def test_simple_deletion1(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AA",
start=31,
alternate_bases=["A"])
assert v.is_indel
assert v.is_deletion
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert self.pg._calculate_length_delta_from_indels(v, []) == 1
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTG"
]
def test_simple_deletion2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AT",
start=32,
alternate_bases=["A"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert panel.alts == [
"ATTAAAGATAGAAATACACGATGCGAGCAACAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_deletion3(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AT",
start=2902618,
alternate_bases=["T"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "TTTATACTACTGCTCAATTTTTTTACTTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNN" in panel.refs
assert panel.alts == [
"TTTATACTACTGCTCAATTTTTTTACTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
def test_simple_deletion4(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert panel.alts == [
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_insertion1(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["TTTC"])
panel = self.pg.create(v)
# assert_no_overlapping_kmers(panel)### Skip this test for vars in first k bases of ref
assert v.is_indel
assert v.is_insertion
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert panel.alts == ["TTTCGATTAAAGATAGAAATACACGATGCGAGC"]
def test_simple_insertion2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["CTTT"])
panel = self.pg.create(v)
# assert_no_overlapping_kmers(panel)### Skip this test for vars in first k bases of ref
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert panel.alts == ["CTTTGATTAAAGATAGAAATACACGATGCGAGCA"]
def test_simple_insertion3(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["ATTT"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCATTTATCAAATTTCATAACATCACCATGAGTTTG"
]
def test_simple_insertion4(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["AGGGG"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert panel.alts == [
"ATTAAAGATAGAAATACACGATGCGAGCAAGGGGTCAAATTTCATAACATCACCATGAGTTTGA"
]
def test_simple_insertion5(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2902618,
alternate_bases=["ATGC"])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "TTTATACTACTGCTCAATTTTTTTACTTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNN" in panel.refs
assert panel.alts == [
"TATACTACTGCTCAATTTTTTTACTTTTATGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
]
def test_double_insertion(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=4021408,
alternate_bases=["ACGCTGGCGGGCG"])
v1 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AGA",
start=4021406,
alternate_bases=["CGG"])
context = [v1]
assert self.pg2._remove_overlapping_contexts(v, [v1]) == []
panel = self.pg2.create(v, context=context)
assert_no_overlapping_kmers(panel)
assert "ATCTAGCCGCAAGGGCGCGAGCAGACGCAGAATCGCATGATTTGAGCTCAAATCATGCGAT" in panel.refs
assert panel.alts == [
"TCTAGCCGCAAGGGCGCGAGCAGACGCAGACGCTGGCGGGCGATCGCATGATTTGAGCTCAAATCATGCGAT"
]
def test_double_indel_fail(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="CCA",
start=2288851,
alternate_bases=["A"])
v1 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2288850,
alternate_bases=["ACC"])
context = [v1]
panel = self.pg2.create(v, context=context)
assert "GGCGCACACAATGATCGGTGGCAATACCGACCACATCGACCTCATCGACGCCGCGTTGCCG" in panel.refs
assert "GGCGCACACAATGATCGGTGGCAATACCGACCACATCGACCTCATCGACGCCGCGTTGCCG" not in panel.alts
def test_large_insertion(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="CCGCCGGCCCCGCCGTTT",
start=1636155,
alternate_bases=[
"CTGCCGGCCCCGCCGGCGCCGCCCAATCCACCGAAGCCCCTCCCTTCGGTGGGGTCGCTGCCGCCGTCGCCGCCGTCACCGCCCTTGCCGCCGGCCCCGCCGTCGCCGCCGGCTCCGGCGGTGCCGTCGCCGCCCTGGCCGCCGGCCCCGCCGTTTCCG"
])
panel = self.pg2.create(v, context=[])
assert_no_overlapping_kmers(panel)
assert "AGACCTAGCAGGGTGCCGGCGCCGCCCTTGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCAT" in panel.refs
assert panel.alts == [
"GACCTAGCAGGGTGCCGGCGCCGCCCTTGCTGCCGGCCCCGCCGGCGCCGCCCAATCCACCGAAGCCCCTCCCTTCGGTGGGGTCGCTGCCGCCGTCGCCGCCGTCACCGCCCTTGCCGCCGGCCCCGCCGTCGCCGCCGGCTCCGGCGGTGCCGTCGCCGCCCTGGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCGCCATCGCCGATGATGTTTTCC"
]
class TestINDELandSNPSAlleleGenerator():
def setup(self):
DB.drop_database('mykrobe-test')
self.pg = AlleleGenerator(
reference_filepath="src/mykrobe/data/BX571856.1.fasta")
self.pg2 = AlleleGenerator(
reference_filepath="src/mykrobe/data/NC_000962.3.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file",
reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref",
md5checksum="sre",
reference_sets=[
self.reference_set])
def teardown(self):
DB.drop_database('mykrobe-test')
def test_ins_with_SNP_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["ATTT"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2])
#assert_no_overlapping_kmers(panel) ### This test seems to fail sometimes, and pass othertimes...
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"GATTAAAGATAGAAATACACGATGCGAGCATTTATCAAATTTCATAACATCACCATGAGTTTG",
"TTAAAGATAGAAATACACGATGCGAGCATTTTTCAAATTTCATAACATCACCATGAGTTTG"])
def test_del_with_SNP_context1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AA",
start=31,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=33,
alternate_bases=["A"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAACAAATTTCATAACATCACCATGAGTTTGA",
"GATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTG"])
def test_del_with_SNP_context2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AA",
start=31,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2]) == []
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert sorted(
panel.alts) == sorted(
["GATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTG"])
def test_del_with_ins_context1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AAT",
start=31,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=4,
alternate_bases=["TTTT"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2]) == [v2]
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTG" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"GATTAAAGATAGAAATACACGATGCGAGCACAAATTTCATAACATCACCATGAGTTTGAT",
"TTTTAAAGATAGAAATACACGATGCGAGCACAAATTTCATAACATCACCATGAGTTTG"])
def test_del_with_ins_context2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["CTTT"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2]) == [v2]
assert self.pg._remove_contexts_not_within_k(v, [v2]) == []
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
["ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context3(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TT"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2]) == [v2]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"TTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context4(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TT"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TG"])
panel = self.pg.create(v, context=[v2, v3])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2, v3]) == [v2, v3]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"TTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"TTGAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context5(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TT"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=6,
alternate_bases=["AG"])
panel = self.pg.create(v, context=[v2, v3])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2, v3]) == [v2, v3]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"TTAGAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGA",
"TTAGAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"TTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context_where_base_is_deleted1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=33,
alternate_bases=["C"])
panel = self.pg.create(v, context=[v2])
assert_no_overlapping_kmers(panel)
assert self.pg._remove_overlapping_contexts(v, [v2]) == []
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
["ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context_where_base_is_deleted2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="TAAA",
start=5,
alternate_bases=["T"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=7,
alternate_bases=["AG"])
panel = self.pg.create(v, context=[v2, v3])
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATC",
"TTAAGAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
panel = self.pg.create(v, context=[v3, v2])
assert_no_overlapping_kmers(panel)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGA" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"ATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATC",
"TTAAGAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGAT"])
def test_snp_with_replace_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="G",
start=2338961,
alternate_bases=["A"])
v1 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="GGATG",
start=2338990,
alternate_bases=["CGATA"])
panel = self.pg2.create(v, context=[v1])
assert_no_overlapping_kmers(panel)
assert "CGACTAGCCACCATCGCGCATCAGTGCGAGGTCAAAAGCGACCAAAGCGAGCAAGTCGCGG" in panel.refs
assert set(panel.alts) == \
set(["CGACTAGCCACCATCGCGCATCAGTGCGAGATCAAAAGCGACCAAAGCGAGCAAGTCGCCG",
"CGACTAGCCACCATCGCGCATCAGTGCGAGATCAAAAGCGACCAAAGCGAGCAAGTCGCGG"])
def test_indel_snp_indel_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="TCGCGTGGC",
start=4021459,
alternate_bases=["GCGAGCAGA"])
v1 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=4021455,
alternate_bases=["ATCTAGCCGCAAG"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=4021489,
alternate_bases=["G"])
panel = self.pg2.create(v) # , context = [v1, v2])
assert_no_overlapping_kmers(panel)
assert "ATCATGCGATTCTGCGTCTGCTCGCGAGGCTCGCGTGGCCGCCGGCGCTGGCGGGCGATCT" in panel.refs
panel = self.pg2.create(v, context=[v1, v2])
assert_no_overlapping_kmers(panel)
assert sorted(
panel.alts) == sorted(
[
"ATCATGCGATTCTGCGTCTGCTCGCGAGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCG",
"ATCATGCGATTCTGCGTCTGCTCGCGAGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCT",
"TGCGTCTGCTCGCGATCTAGCCGCAAGGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCG",
"TGCGTCTGCTCGCGATCTAGCCGCAAGGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCT"])
def test_complex_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATTT",
start=1503643,
alternate_bases=["A"])
v1 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="CCT",
start=1503615,
alternate_bases=["C"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=1503655,
alternate_bases=["ATGCCGCCGCC"])
panel = self.pg2.create(v, context=[v1, v2])
assert_no_overlapping_kmers(panel)
assert "ATCCTGGAGCCCACCAGCGGAAACACCGGCATTTCGCTGGCGATGGCGGCCCGGTTGAAGG" in panel.refs
assert set(panel.alts) == set([
"CCATCGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGGCGGCCCGGTTGAAGGGGT",
"TCCTGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGGCGGCCCGGTTGAAGGGG",
"ATCGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGCCGCCGCCTGGCGGCCCGG",
"TCCTGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGCCGCCGCCTGGCGGCCCGG",
])
def test_panel_generator(self):
pg = AlleleGenerator(
reference_filepath="src/mykrobe/data/BX571856.1.fasta")
assert pg.ref is not None
class TestSNPAlleleGenerator():
def setup(self):
DB.drop_database('mykrobe-test')
self.pg = AlleleGenerator(
reference_filepath="src/mykrobe/data/BX571856.1.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def test_panel_generator(self):
pg = AlleleGenerator(
reference_filepath="src/mykrobe/data/BX571856.1.fasta")
assert pg.ref is not None
def test_simple_variant(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT"
]
assert self.pg._calculate_length_delta_from_indels(v, []) == 0
assert v.is_indel is False
def test_simple_variant2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC"
]
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGATC"
]
def test_simple_variant_invalid(self):
with pytest.raises(ValueError) as cm:
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=31,
alternate_bases=["T"])
panel = self.pg.create(v)
def test_simple_variant_start(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"
]
assert panel.alts == [
"TGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_variant_end(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2902618,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTAT"
]
assert panel.alts == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTTT"
]
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=2902616,
alternate_bases=["C"])
panel = self.pg.create(v)
assert panel.refs == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTAT"
]
assert panel.alts == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTCTAT"
]
def test_simple_variant_with_nearby_snp(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2])
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT"
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
v3 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"])
panel = self.pg.create(v, context=[v2, v3])
assert panel.refs == [
'CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT',
'CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT',
'CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT',
'CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT'
]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_variant_with_multiple_nearby_snps2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
v3 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"])
v4 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"])
v5 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["A"])
assert sorted(self.pg._split_context([v, v3, v4])) == sorted([[v, v4],
[v, v3]])
assert (self.pg._split_context([v3, v4])) == [[v4], [v3]]
assert (self.pg._split_context([v, v3, v4, v5])) == [[v, v4, v5],
[v, v3, v5]]
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert sorted(panel.refs) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGAAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGAATTCAAATTTCATAACATCACCATGAGTTTGAT"
])
assert sorted(panel.alts) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGATATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGATTTCAAATTTCATAACATCACCATGAGTTTGAT"
])
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
v5 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["G"])
v3 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"])
v4 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert sorted(panel.refs) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCAGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTAGTCAAATTTCATAACATCACCATGAGTTTGAT"
])
assert sorted(panel.alts) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTGTCAAATTTCATAACATCACCATGAGTTTGAT"
])
def test_panel_generator(self):
pg = AlleleGenerator(reference_filepath=f"{DATA_DIR}/BX571856.1.fasta",
kmer=31)
assert pg.ref is not None
def run(parser, args):
# There's no need to try to connect to database if we're not doing backgrounds
if args.no_backgrounds:
logger.info(
"Not connecting to database, because --no-backgrounds option used")
DB = None
else:
DB = connect("%s-%s" % (DB_PREFIX, args.db_name))
if DB is not None:
try:
Variant.objects()
logger.info("Connected to %s-%s" % (DB_PREFIX, args.db_name))
except (ServerSelectionTimeoutError):
DB = None
logger.warning(
"Could not connect to database. Continuing without using genetic backgrounds"
)
mutations = []
lineages = set()
reference = os.path.basename(args.reference_filepath).split(".fa")[0]
if args.vcf:
run_make_probes_from_vcf_file(args)
elif args.genbank:
aa2dna = GeneAminoAcidChangeToDNAVariants(args.reference_filepath,
args.genbank)
if args.text_file:
with open(args.text_file, "r") as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene, mutation_string, alphabet = row
if alphabet == "DNA":
protein_coding_var = False
else:
protein_coding_var = True
for var_name in aa2dna.get_variant_names(
gene, mutation_string, protein_coding_var):
mutation = Mutation(
reference=reference,
var_name=var_name,
gene=aa2dna.get_gene(gene),
mut=mutation_string,
protein_coding_var=protein_coding_var,
)
mutations.append(mutation)
else:
for variant in args.variants:
gene, mutation = variant.split("_")
for var_name in aa2dna.get_variant_names(gene, mutation):
mutations.append(
Mutation(
reference=reference,
var_name=var_name,
gene=gene,
mut=mutation,
))
else:
if args.text_file:
mutations, lineages = load_dna_vars_txt_file(
args.text_file, reference)
if args.lineage:
with open(args.lineage, "w") as f:
json.dump(lineages, f, sort_keys=True, indent=2)
else:
mutations.extend(
Mutation(reference=reference, var_name=v)
for v in args.variants)
al = AlleleGenerator(reference_filepath=args.reference_filepath,
kmer=args.kmer)
for enum, mut in enumerate(mutations):
if enum % 100 == 0:
logger.info(
"%i of %i - %f%%" %
(enum, len(mutations), round(100 * enum / len(mutations), 2)))
variant_panel = make_variant_probe(al,
mut.variant,
args.kmer,
DB=DB,
no_backgrounds=args.no_backgrounds)
if variant_panel is not None:
for i, ref in enumerate(variant_panel.refs):
try:
gene_name = mut.gene.name
except AttributeError:
gene_name = "NA"
sys.stdout.write(
">ref-%s?var_name=%s&num_alts=%i&ref=%s&enum=%i&gene=%s&mut=%s\n"
% (
mut.mutation_output_name,
mut.variant.var_name,
len(variant_panel.alts),
mut.reference,
i,
gene_name,
mut.mutation_output_name,
))
sys.stdout.write("%s\n" % ref)
for i, a in enumerate(variant_panel.alts):
sys.stdout.write(
">alt-%s?var_name=%s&enum=%i&gene=%s&mut=%s\n" % (
mut.mutation_output_name,
mut.variant.var_name,
i,
gene_name,
mut.mutation_output_name,
))
sys.stdout.write("%s\n" % a)
else:
logger.warning("All variants failed for %s_%s - %s" %
(mut.gene, mut.mutation_output_name, mut.variant))
class TestLargeINDELAlleleGenerator():
def setup(self):
DB.drop_database('mykrobe-test')
self.pg = AlleleGenerator(
reference_filepath=f"{DATA_DIR}/NC_000962.3.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def test_large_variant1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"AACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACT",
start=1355983,
alternate_bases=[
"ACCGCCCGGTATCTGAGGATTGGTTTTCCACCCAAATACAAGTCGCATTCGCG"
])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "TCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGA" in panel.refs
assert panel.alts == [
"TCGTCACCGCCCGGTATCTGAGGATTGGTTTTCCACCCAAATACAAGTCGCATTCGCGGGA"
]
def test_large_variant2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"AACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCAC",
start=1355983,
alternate_bases=[
"ACCGCCCGGTATCTGAGGATTGGTTTTCCACCCAAATACAAGTCGCATTCGC"
])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "TCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGA" in panel.refs
assert panel.alts == [
"TCGTCACCGCCCGGTATCTGAGGATTGGTTTTCCACCCAAATACAAGTCGCATTCGCTGGA"
]
# def test_large_variant3(self):
# v = Variant.create(
# variant_sets=self.variant_sets,
# reference=self.reference,
# reference_bases="TCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGA",
# start=1355978,
# alternate_bases=["TCGTCAACGCCCGGTATCTGAGGATCGGTGTTCTCACCCAATACAAGTCGCATTCACTGGA"])
# panel = self.pg.create(v)
# assert_no_overlapping_kmers(panel)
# assert "CAAACCTCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCA" in panel.refs
# assert panel.alts == [
# "CAAACCTCGTCAACGCCCGGTATCTGAGGATCGGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCA"]
# def test_very_large_variant3(self):
# v = Variant.create(
# variant_sets=self.variant_sets,
# reference=self.reference,
# reference_bases="TCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCAT",
# start=1355978,
# alternate_bases=["TCGTCAACGCCCGGTATCTGAGGATCGGTGTTCACCCAATACAAGTCGCATTCACTGGACCGCCAT"])
# panel = self.pg.create(v)
# assert "AAACCTCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCATATCTCG" in panel.refs
# assert panel.alts == [
# "CAAACCTCGTCAACGCCCGGTATCTGAGGATCGGTGTTCACCCAATACAAGTCGCATTCACTGGACCGCCATATCTCGC"]
def test_large_insertion(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=2352065,
alternate_bases=[
"CCTCGCCTGGGCTGGCGAGCAGACGCAAAATCCCCCGCACGCCCGGCGTGTCGGGGGATTTTGCGTCTG"
])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "AGCTCGGCCAGCTCAGTCACGTCGCCGCCGCCTCGCCAGTTGACCGCGCCCGCTCGCGGCT" in panel.refs
assert panel.alts == [
"CCAGCTCAGTCACGTCGCCGCCGCCTCGCCTGGGCTGGCGAGCAGACGCAAAATCCCCCGCACGCCCGGCGTGTCGGGGGATTTTGCGTCTGCTCGCCAGTTGACCGCGCCCGCTCGCGGCT"
]
def test_large_var1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"CGCGGGAGTAGAACGATCGCCAAGTGGTCGGTCTTGGCTGCCCACTTCATCCCCGGCGCCACCGGCAGGTCTCGCGGTCATCTCGACCAACGGAGGGCCGTCGGTGGTTCGTATCCGGCCAAGAACGGCGAGAACGGTTTGTGCCTCTATGCCAGGGTGAATGTCTCATCTCCCAGGCGGACGGTGATATCCAGTTCTCCGCCAAGAGCGGACACGTATTTGCGCAGTGTGTTGACCTGTGCGGAGCCGATGTCGCCGTTCTCGATGCTGGATACCCGGCTCTGCCGGATGTGCGCCAGCGCAGCCACCTGGACCTGGGTGAGTGACTGAGCCGCGCGCAGCTCCCGGAGCCGGAATGCCCGCACTTCATCGCGCATTCGTGCCTTGTGCCGGTCCACCGCCTCCCGGTTAACGGGACGTACGGCGTCCATGTCCCGTAGTGTCATCGCCATCGTGCCACTTACCCTTTCTTGCGCTTGCGCCTCTTTGGCTTCGTGTCCTCGAACTGTGCGAGATGTTCGGCAAACATCTCATCGGCCGCTTTGATCTTCTCGTCGTACCACTGGGTCCACCGCCCGGCCTTGTTACCGGCGGCCAGCATGATCGCCTGCCGCGCCGGGTCGAAGGCGAACAGAATGCGGACCTCGGACCGCCCTTGTGATCCTGGACGCAGCTCCTTCATGTTCTTGTGGCGCGACCCACGCACCGTGTCCACCAGAGGACAGCCAAGTGCGGGGCCCTCTTCCTCGAGAACCTCGATAGCTGCGAACACCAATTCGTAGGTCTCTCGGTCCAAGCCGTTGAGCCAGGCGGAGATGCGCTCCACATCCGCCGTCCACCCCACAGAGTCGCAGAGTAGCGCGATACGCGATATCACACAAGGGTGATATTCCTCCGGGTAAGAGCAGCGGGCGACGGGGCTACCGTCGAGGAAATGCCGGCAGGCGAGGACGGACTCTGCGCACCCGGGCCGTTGAAACAGTAGCCTGTGCCAGGCCGAGAATTCATCCCCACGTATGAGGCAGTACAGTGCGCCGCCGTGCGCGTTCTCCCATGGAACGTTCACGGGCTCCCGTGGATGACAGGCGTTTCATGAACGCCAGCGCCGCCGCAACCCGACCGAAAGCGGTTGACCCCAAGGAGAGCTGGAAGTCGAGGCCACCACCTTCGCCGCGGAGTTGCTCATGCCCGAGAGCGAGACTCGTCCCGAAATACGCCGGCTCGATTTCGGCAAGTTGCTCGAACTGAAGCGGGAATGGGCGTCGACCCGCTCGACCAGCCCCAGCCGGGTGACCAGCCCCAGCCGGGTGACCAGCCGATGCACCGCGGCGATCCCACCGAAGCCGGTGGCATCGATGTTGGCGCCGACCTCGTAGCGCACCGCGCCCGAACCCAGCATCGGCCTGGGCTGCGCCGCCCAGCGTCCAGCCCGCGCGTGCCGCGCCGCCACCCTGCGCCCTCGGCGTGTGATGTTTCGCCGACTCTGTTCATGGGTTATCTTCTTCACCACAAAGGCCTTTCCTGCTGGGCTGTGTTGAGGTCGCAAACCCAGCCAGGGTAAGGCCTTTGGCCTCTCCTACCCGGCCGACACGCTTACTGAAGGCCTAGTCTAGGCAGGCCATTCAATCTGCGGAATCGAAAAATTCGGTTCCAGCCTGCTCGTTTCCTTTCCGACAGCGATCTGACGTTGCGTAACGTCATTTGTACGGACTCTTTTAGCGGCATTGATTTCAGATGCCAACGCCGTCTGTGCTGTAGCGCCGATTGGCCGAAACTGTAAATTTGTATGATTATTTAAATCTTTGACGAACACGCGCCACAAACGTACTATCTCTTTGGCAAAGTCCACCGGCATCTCATTCAACGGTTTTGTTTGCGCGTGGTCGTCATATGTTGGTAACTGTGTAACCGGCCGCCTATCTTGCGCGTGCATCATATGACTATGAATCGGCCTTCTCCAGTGAAATTGATACAAGATCGATCCGATAAGCGGTACCTTGTACACAGTGCAATTGTAGTAATTCGCGTTTTGTCCTACGCTTGTATTCTGCGTGAAGAATTCA",
start=2266659,
alternate_bases=[
"CACGCGAGTTGTAGATGATCGTTGAGTGGTCTTGCTTGGACTTCCATTTCATCTTTTCGACGCGCCAGGTCTCGCGGTCCTCCGGATCTGCGCCCGGTTTGAGTTGCACATCAAGGGGATACGGCTTGACCGACTCGTAGCCGACATGTAAGTCGGCTAGTTTCCGGCCGGCGCTGGCGAGCTGGTCGAAGCGTTCGCGGGTCTCCGGTGTTGGGATGTGCGGGAGCATCTTCTTGAGGTCAGCGGCGTATTTTGTGCGGTAGGCGGGGTCATGCAGCAGGCCGTAGACGTAGTAGAAGATGTCGTCTTTGGTGACTTGGTCGCCGATCGTGTCGCGGTAGAGCTTGAGGATGACGCCGGTGATGTTGTCGACGCGGCGGTAGCCGTGGTCGTCTACTTCGGCGTTGGTGGTGGACTCGAAATCGAGTTCGCCGTCACGTGGTTCGGTCTTCTCGTAGGTCCAGCGCGGGAAGAATTGACCGTTGCTTGAGCCCCAGAATGCGAGATCGGGGATAGCGTTTAGCATCAGACACGAGAAGGGCTTGTCTGAGCCCATGCCAACCACGTAGTAACCGACATTCCCGTGCTCCGGCGTCGGAAACATCGACGGAAGCTGGTAGGTACAGTTGTTGAGCTGCTGGTTGGGGTCGAGGTAGGCGTGCTCTTTCGTAAATGGTCGGTACGTGCCGAGCCGCATTCCCGCGGGAGCGAATTCGATGCGAATGCCTTGTGCCACTTGCCGCTTGTTGATGCGGTCCCAGCTGAACTTGGCCGAGTCCACGGTAATGAGGGCGTCAACCGGCGGGGTCTTGGCGTCCCTTCCGCGGATCTCGTTGATCCGGTCGACCTCCGAGTTGTAGAAGTCGATCGTGCGTCCGATGTTGGCCTCGAGCGCACCACGTGAAAAGTTGTAACACCACGCATCCCGGCTGGTCTTCAAGCCCGCGGAATAGTTCGCGAAGACACGTGTCACGTCAAGAGCAGCCTTCTTGTCGCCGATAACCGGCCACGCGCTGAACGCGTCGTCGCGTTGGTTGACCCAGTCACCGTGCAAGTTGGGTGTGACTGTCTGCCATTCCACCGTGTCGAGGTAGCCGTCGCCGACGATCCGCAACTTCTCCTCGCGACTCAGGTAATCGCCGATGTCGCGGTAAAGGACATCGCATGGCCCGCTGTGCTTCGGATCCTTGATGCCAAGGAAGATCGCCACCGTGTTGCGACTCCCCCCGCCAAAGACCTTGCCGCCTTCCTGGCGTGAGAGTTCCCCAGCTGTGCGCTGGTTCCCCCGCAGGTTGTACACATATACCGCCGCGTAGTCGTCGGCGAGCGACAACCGCATGCCGTCTGCCGTGTTGCCGTCTATGTACCCACCATTGGAGACGAATCCGACAACACCGTTGTCACCAATGCGGTCGGTCGCCCACCGGAACGCGCGAATATACGAGTCGTACAGGCTGTTCTTCAGCTGCGCCGTCGACCGCTTCGCGTACGTCTGCTCAATCCGCCCGTCCAACGTCGGATACTTCACGTTGGCGTTCAGGTCGTTCGCGCTGCTCTGCCCCACCGAGTACGGCGGATTCCCGATGATCACGCTGATCGGCGTCGCCAGCTGTCGCAAGATCCGAGCGTTGTTGTACGGGAACATGATCGCGTCCATCGAGTCCCCGGCTTCGGAAATCTGGAACGTGTCGGCCAGCGCCATCCCGGGGAACGGCTCATAGGCGTCGGCGTCGGCGGTCTTGCCCGCCAAAGCATGGTAGGTCGACTCGATGTTCACCGCGGCGATGTAGTACGCCAGCAGCATGATCTCGTTGGCGTGCAGCTCTTGCGAGTACTTTCGGGTGAGGTCGGCGGCCGTGATCAGGTCGGACTGCAGCAGCCGGGTAATGAATGTGCCCGTCCCGGCGAAGCCGTCCAGAATATGCACGCCCTCGTCGGTCAGCCCGCGCCCGAAATGCTTGCGCGACACGAAATCAGCCGCCCGCACAATGAAGTCCACGACCTCGACCGGCGTGTACACGATCCCCAGCGCCTCGGCCTGCTTCTTGAAGCCGATGCGGAAGAACTTCTCGTACAGCTCGGCGATCACCTGCTGCTTGCCCTCGGCGCTGGTGACCTCGCCGGCGCGCCGTCGCACCGATTCGTAAAAGCCTTCCAACCGAGCGGTTTCGGCCTCCAGGCCGGCACCCCCGACGGTGTCGACCATCTTCTGCATGGCCCGCGACACCGGGTTGTGCGACGCGAAGTCATGCCCGGCGAACAGCGCGTCGAACACCGGCTTGGTGATCAGGTGCTGCGAGAGCATGCTGATCGCGTCATCGGGGGTGATCGAGTCATTGAGGTTATCGCGCAGCCCGGCCAGGAACTGCTCGAACGCCGCCGCCGCCGTAGCGTCGGCGCCGCCGAGCAGGGCGTGGATACGGGTGGTCAGCGTCGCGGCGATGTCGGCGACATCGGCGGCCCACTGCTCCCAATAGGTCCGGGTGCCAACCTTGTCGACGATGCGCGCGTAGATCGCTTCCTGCCACTGCGACAACGAGAACATCGCCAACTGCTCCGCGACGGCGGGTCCCGCCTCGTCGGAGGTCGGCCCGATGTGACCGCCCAACAGCTTGTCGCTGCCTTCACCGGTCTTCGTCGGCTTCACGTTCAGCGCAATGCTGTTCACCATCGCGTCGAAGCGCTCGTCGTGCGACCGCAACGCGTTGAGGACCTGCCACACCACCTTGAACCGTTTGTTGTCGGCCAACGCGGCAGACGGCTCGACACCCTCGGGCACCGCCACCGGCAAGATGACGTACCCGTAGTCCTTGCCGGGCGACTTGCGCATCACCCGACCGACCGACTGCACCACGTCGACGATGGAATTGCGCGGATTCAGGAACAGCACCGCGTCCAGCGCGGGCACGTCGACCCCTTCGGAGAGGCAGCGGGCGTTGGACAGGATGCGGCATTCATCCTCGGCGACCACGCCTTTGAGCCAGGCCAGCTGTTCGTTGCGGACCAGCGCGTTGAACGTCCCGTCCACGTGGCGCACCG"
])
panel = self.pg.create(v)
assert_no_overlapping_kmers(panel)
assert "TGGTGACGCGGGAGTAGAACGATCGCCAAGTGGTCGGTCTTGGCTGCCCACTTCATCCCCGGCGCCACCGGCAGGTCTCGCGGTCATCTCGACCAACGGAGGGCCGTCGGTGGTTCGTATCCGGCCAAGAACGGCGAGAACGGTTTGTGCCTCTATGCCAGGGTGAATGTCTCATCTCCCAGGCGGACGGTGATATCCAGTTCTCCGCCAAGAGCGGACACGTATTTGCGCAGTGTGTTGACCTGTGCGGAGCCGATGTCGCCGTTCTCGATGCTGGATACCCGGCTCTGCCGGATGTGCGCCAGCGCAGCCACCTGGACCTGGGTGAGTGACTGAGCCGCGCGCAGCTCCCGGAGCCGGAATGCCCGCACTTCATCGCGCATTCGTGCCTTGTGCCGGTCCACCGCCTCCCGGTTAACGGGACGTACGGCGTCCATGTCCCGTAGTGTCATCGCCATCGTGCCACTTACCCTTTCTTGCGCTTGCGCCTCTTTGGCTTCGTGTCCTCGAACTGTGCGAGATGTTCGGCAAACATCTCATCGGCCGCTTTGATCTTCTCGTCGTACCACTGGGTCCACCGCCCGGCCTTGTTACCGGCGGCCAGCATGATCGCCTGCCGCGCCGGGTCGAAGGCGAACAGAATGCGGACCTCGGACCGCCCTTGTGATCCTGGACGCAGCTCCTTCATGTTCTTGTGGCGCGACCCACGCACCGTGTCCACCAGAGGACAGCCAAGTGCGGGGCCCTCTTCCTCGAGAACCTCGATAGCTGCGAACACCAATTCGTAGGTCTCTCGGTCCAAGCCGTTGAGCCAGGCGGAGATGCGCTCCACATCCGCCGTCCACCCCACAGAGTCGCAGAGTAGCGCGATACGCGATATCACACAAGGGTGATATTCCTCCGGGTAAGAGCAGCGGGCGACGGGGCTACCGTCGAGGAAATGCCGGCAGGCGAGGACGGACTCTGCGCACCCGGGCCGTTGAAACAGTAGCCTGTGCCAGGCCGAGAATTCATCCCCACGTATGAGGCAGTACAGTGCGCCGCCGTGCGCGTTCTCCCATGGAACGTTCACGGGCTCCCGTGGATGACAGGCGTTTCATGAACGCCAGCGCCGCCGCAACCCGACCGAAAGCGGTTGACCCCAAGGAGAGCTGGAAGTCGAGGCCACCACCTTCGCCGCGGAGTTGCTCATGCCCGAGAGCGAGACTCGTCCCGAAATACGCCGGCTCGATTTCGGCAAGTTGCTCGAACTGAAGCGGGAATGGGCGTCGACCCGCTCGACCAGCCCCAGCCGGGTGACCAGCCCCAGCCGGGTGACCAGCCGATGCACCGCGGCGATCCCACCGAAGCCGGTGGCATCGATGTTGGCGCCGACCTCGTAGCGCACCGCGCCCGAACCCAGCATCGGCCTGGGCTGCGCCGCCCAGCGTCCAGCCCGCGCGTGCCGCGCCGCCACCCTGCGCCCTCGGCGTGTGATGTTTCGCCGACTCTGTTCATGGGTTATCTTCTTCACCACAAAGGCCTTTCCTGCTGGGCTGTGTTGAGGTCGCAAACCCAGCCAGGGTAAGGCCTTTGGCCTCTCCTACCCGGCCGACACGCTTACTGAAGGCCTAGTCTAGGCAGGCCATTCAATCTGCGGAATCGAAAAATTCGGTTCCAGCCTGCTCGTTTCCTTTCCGACAGCGATCTGACGTTGCGTAACGTCATTTGTACGGACTCTTTTAGCGGCATTGATTTCAGATGCCAACGCCGTCTGTGCTGTAGCGCCGATTGGCCGAAACTGTAAATTTGTATGATTATTTAAATCTTTGACGAACACGCGCCACAAACGTACTATCTCTTTGGCAAAGTCCACCGGCATCTCATTCAACGGTTTTGTTTGCGCGTGGTCGTCATATGTTGGTAACTGTGTAACCGGCCGCCTATCTTGCGCGTGCATCATATGACTATGAATCGGCCTTCTCCAGTGAAATTGATACAAGATCGATCCGATAAGCGGTACCTTGTACACAGTGCAATTGTAGTAATTCGCGTTTTGTCCTACGCTTGTATTCTGCGTGAAGAATTCAAACA" in panel.refs
assert panel.alts == [
"GGCCTCGTCGGGAATGCCGGCGATGGTGACACGCGAGTTGTAGATGATCGTTGAGTGGTCTTGCTTGGACTTCCATTTCATCTTTTCGACGCGCCAGGTCTCGCGGTCCTCCGGATCTGCGCCCGGTTTGAGTTGCACATCAAGGGGATACGGCTTGACCGACTCGTAGCCGACATGTAAGTCGGCTAGTTTCCGGCCGGCGCTGGCGAGCTGGTCGAAGCGTTCGCGGGTCTCCGGTGTTGGGATGTGCGGGAGCATCTTCTTGAGGTCAGCGGCGTATTTTGTGCGGTAGGCGGGGTCATGCAGCAGGCCGTAGACGTAGTAGAAGATGTCGTCTTTGGTGACTTGGTCGCCGATCGTGTCGCGGTAGAGCTTGAGGATGACGCCGGTGATGTTGTCGACGCGGCGGTAGCCGTGGTCGTCTACTTCGGCGTTGGTGGTGGACTCGAAATCGAGTTCGCCGTCACGTGGTTCGGTCTTCTCGTAGGTCCAGCGCGGGAAGAATTGACCGTTGCTTGAGCCCCAGAATGCGAGATCGGGGATAGCGTTTAGCATCAGACACGAGAAGGGCTTGTCTGAGCCCATGCCAACCACGTAGTAACCGACATTCCCGTGCTCCGGCGTCGGAAACATCGACGGAAGCTGGTAGGTACAGTTGTTGAGCTGCTGGTTGGGGTCGAGGTAGGCGTGCTCTTTCGTAAATGGTCGGTACGTGCCGAGCCGCATTCCCGCGGGAGCGAATTCGATGCGAATGCCTTGTGCCACTTGCCGCTTGTTGATGCGGTCCCAGCTGAACTTGGCCGAGTCCACGGTAATGAGGGCGTCAACCGGCGGGGTCTTGGCGTCCCTTCCGCGGATCTCGTTGATCCGGTCGACCTCCGAGTTGTAGAAGTCGATCGTGCGTCCGATGTTGGCCTCGAGCGCACCACGTGAAAAGTTGTAACACCACGCATCCCGGCTGGTCTTCAAGCCCGCGGAATAGTTCGCGAAGACACGTGTCACGTCAAGAGCAGCCTTCTTGTCGCCGATAACCGGCCACGCGCTGAACGCGTCGTCGCGTTGGTTGACCCAGTCACCGTGCAAGTTGGGTGTGACTGTCTGCCATTCCACCGTGTCGAGGTAGCCGTCGCCGACGATCCGCAACTTCTCCTCGCGACTCAGGTAATCGCCGATGTCGCGGTAAAGGACATCGCATGGCCCGCTGTGCTTCGGATCCTTGATGCCAAGGAAGATCGCCACCGTGTTGCGACTCCCCCCGCCAAAGACCTTGCCGCCTTCCTGGCGTGAGAGTTCCCCAGCTGTGCGCTGGTTCCCCCGCAGGTTGTACACATATACCGCCGCGTAGTCGTCGGCGAGCGACAACCGCATGCCGTCTGCCGTGTTGCCGTCTATGTACCCACCATTGGAGACGAATCCGACAACACCGTTGTCACCAATGCGGTCGGTCGCCCACCGGAACGCGCGAATATACGAGTCGTACAGGCTGTTCTTCAGCTGCGCCGTCGACCGCTTCGCGTACGTCTGCTCAATCCGCCCGTCCAACGTCGGATACTTCACGTTGGCGTTCAGGTCGTTCGCGCTGCTCTGCCCCACCGAGTACGGCGGATTCCCGATGATCACGCTGATCGGCGTCGCCAGCTGTCGCAAGATCCGAGCGTTGTTGTACGGGAACATGATCGCGTCCATCGAGTCCCCGGCTTCGGAAATCTGGAACGTGTCGGCCAGCGCCATCCCGGGGAACGGCTCATAGGCGTCGGCGTCGGCGGTCTTGCCCGCCAAAGCATGGTAGGTCGACTCGATGTTCACCGCGGCGATGTAGTACGCCAGCAGCATGATCTCGTTGGCGTGCAGCTCTTGCGAGTACTTTCGGGTGAGGTCGGCGGCCGTGATCAGGTCGGACTGCAGCAGCCGGGTAATGAATGTGCCCGTCCCGGCGAAGCCGTCCAGAATATGCACGCCCTCGTCGGTCAGCCCGCGCCCGAAATGCTTGCGCGACACGAAATCAGCCGCCCGCACAATGAAGTCCACGACCTCGACCGGCGTGTACACGATCCCCAGCGCCTCGGCCTGCTTCTTGAAGCCGATGCGGAAGAACTTCTCGTACAGCTCGGCGATCACCTGCTGCTTGCCCTCGGCGCTGGTGACCTCGCCGGCGCGCCGTCGCACCGATTCGTAAAAGCCTTCCAACCGAGCGGTTTCGGCCTCCAGGCCGGCACCCCCGACGGTGTCGACCATCTTCTGCATGGCCCGCGACACCGGGTTGTGCGACGCGAAGTCATGCCCGGCGAACAGCGCGTCGAACACCGGCTTGGTGATCAGGTGCTGCGAGAGCATGCTGATCGCGTCATCGGGGGTGATCGAGTCATTGAGGTTATCGCGCAGCCCGGCCAGGAACTGCTCGAACGCCGCCGCCGCCGTAGCGTCGGCGCCGCCGAGCAGGGCGTGGATACGGGTGGTCAGCGTCGCGGCGATGTCGGCGACATCGGCGGCCCACTGCTCCCAATAGGTCCGGGTGCCAACCTTGTCGACGATGCGCGCGTAGATCGCTTCCTGCCACTGCGACAACGAGAACATCGCCAACTGCTCCGCGACGGCGGGTCCCGCCTCGTCGGAGGTCGGCCCGATGTGACCGCCCAACAGCTTGTCGCTGCCTTCACCGGTCTTCGTCGGCTTCACGTTCAGCGCAATGCTGTTCACCATCGCGTCGAAGCGCTCGTCGTGCGACCGCAACGCGTTGAGGACCTGCCACACCACCTTGAACCGTTTGTTGTCGGCCAACGCGGCAGACGGCTCGACACCCTCGGGCACCGCCACCGGCAAGATGACGTACCCGTAGTCCTTGCCGGGCGACTTGCGCATCACCCGACCGACCGACTGCACCACGTCGACGATGGAATTGCGCGGATTCAGGAACAGCACCGCGTCCAGCGCGGGCACGTCGACCCCTTCGGAGAGGCAGCGGGCGTTGGACAGGATGCGGCATTCATCCTCGGCGACCACGCCTTTGAGCCAGGCCAGCTGTTCGTTGCGGACCAGCGCGTTGAACGTCCCGTCCACGTGGCGCACCGAACACGCCAGGCCCGGGCCGTCGTCAACCA"
]
def run(parser, args):
DB = connect('mykrobe-%s' % (args.db_name))
if DB is not None:
try:
Variant.objects()
logging.info(
"Connected to mykrobe-%s" % (args.db_name))
except (ServerSelectionTimeoutError):
DB = None
logging.warning(
"Could not connect to database. Continuing without using genetic backgrounds")
mutations = []
reference = os.path.basename(args.reference_filepath).split('.fa')[0]
if args.vcf:
run_make_probes_from_vcf_file(args)
elif args.genbank:
aa2dna = GeneAminoAcidChangeToDNAVariants(
args.reference_filepath,
args.genbank)
if args.text_file:
with open(args.text_file, 'r') as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene, mutation_string, alphabet = row
if alphabet == "DNA":
protein_coding_var = False
else:
protein_coding_var = True
for var_name in aa2dna.get_variant_names(
gene, mutation_string, protein_coding_var):
mutation = Mutation(reference=reference,
var_name=var_name,
gene=aa2dna.get_gene(gene),
mut=mutation_string)
mutations.append(mutation)
else:
for variant in args.variants:
gene, mutation = variant.split("_")
for var_name in aa2dna.get_variant_names(gene, mutation):
mutations.append(
Mutation(reference=reference,
var_name=var_name,
gene=gene,
mut=mutation))
else:
if args.text_file:
with open(args.text_file, 'r') as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene_name, pos, ref, alt, alphabet = row
if gene_name == "ref":
mutations.append(
Mutation(
reference=reference,
var_name="".join([ref, pos, alt])))
else:
mutations.append(
Mutation(
reference=reference,
var_name=row[0]))
else:
mutations.extend(Mutation(reference=reference, var_name=v)
for v in args.variants)
al = AlleleGenerator(
reference_filepath=args.reference_filepath,
kmer=args.kmer)
for enum, mut in enumerate(mutations):
if enum % 100 == 0:
logger.info(
"%i of %i - %f%%" % (enum, len(mutations), round(100*enum/len(mutations), 2)))
variant_panel = make_variant_probe(
al, mut.variant, args.kmer, DB=DB, no_backgrounds=args.no_backgrounds)
if variant_panel is not None:
for i, ref in enumerate(variant_panel.refs):
try:
gene_name = mut.gene.name
except AttributeError:
gene_name = "NA"
sys.stdout.write(
">ref-%s?var_name=%s&num_alts=%i&ref=%s&enum=%i&gene=%s&mut=%s\n" %
(mut.mut, mut.variant.var_name, len(
variant_panel.alts), mut.reference, i, gene_name, mut.mut))
sys.stdout.write("%s\n" % ref)
for i, a in enumerate(variant_panel.alts):
sys.stdout.write(">alt-%s?var_name=%s&enum=%i&gene=%s&mut=%s\n" %
(mut.mut, mut.variant.var_name, i, gene_name, mut.mut))
sys.stdout.write("%s\n" % a)
else:
logging.warning(
"All variants failed for %s_%s - %s" %
(mut.gene, mut.mut, mut.variant))
