def add_snp(options, snp, position, sequence):
if snp.alt != ".":
genotype = "".join(vcfwrap.get_ml_genotype(snp, options.nth_sample))
encoded = sequences.encode_genotype(genotype)
else:
encoded = snp.ref
sequence[position] = encoded
def filter_singletons(self, to_filter, filter_using):
included, excluded, to_filter \
= self._group(filter_using, to_filter)
sequence = list(to_filter.sequence)
sequences = [record.sequence.upper() for record in included]
for (index, nts) in enumerate(zip(*sequences)):
current_nt = sequence[index].upper()
if current_nt in "N-":
continue
allowed_nts = set()
for allowed_nt in nts:
if allowed_nt not in "N-":
allowed_nts.update(NT_CODES[allowed_nt])
filtered_nts = frozenset(NT_CODES[current_nt]) & allowed_nts
if not filtered_nts:
filtered_nts = "N"
genotype = encode_genotype(filtered_nts)
if genotype != current_nt:
sequence[index] = genotype.lower()
new_record = FASTA(to_filter.name, to_filter.meta, "".join(sequence))
return MSA([new_record] + included + excluded)
def filter_singletons(self, to_filter, filter_using):
included, excluded, to_filter \
= self._group(filter_using, to_filter)
sequence = list(to_filter.sequence)
sequences = [record.sequence.upper() for record in included]
for (index, nts) in enumerate(zip(*sequences)):
current_nt = sequence[index].upper()
if current_nt in "N-":
continue
allowed_nts = set()
for allowed_nt in nts:
if allowed_nt not in "N-":
allowed_nts.update(NT_CODES[allowed_nt])
filtered_nts = frozenset(NT_CODES[current_nt]) & allowed_nts
if not filtered_nts:
filtered_nts = "N"
genotype = encode_genotype(filtered_nts)
if genotype != current_nt:
sequence[index] = genotype.lower()
new_record = FASTA(to_filter.name,
to_filter.meta,
"".join(sequence))
return MSA([new_record] + included + excluded)
def add_snp(options, snp, position, sequence):
if snp.alt != ".":
genotype = "".join(vcfwrap.get_ml_genotype(snp, options.nth_sample))
encoded = sequences.encode_genotype(genotype)
else:
encoded = snp.ref
sequence[position] = encoded
def test_genotype__bad_input(value):
with pytest.raises(ValueError):
encode_genotype(value)
def test_genotype__bad_input__mixedcase():
encode_genotype("At")
def test_genotype__bad_input__lowercase():
encode_genotype("a")
def test_function(src, dst):
assert_equal(encode_genotype(src), dst)
def test_function(sequence):
assert_equal(encode_genotype(sequence), "Y")
def test_genotype__bad_input__non_nucleotide():
encode_genotype("+")
def test_genotype__bad_input__non_nucleotide():
encode_genotype("+")
def test_genotype__permutations(src, dst):
for seq in itertools.permutations(src):
assert encode_genotype("".join(src)) == dst
def test_comma_or_not(sequence):
assert encode_genotype(sequence) == "Y"
def test_genotype__bad_input__mixedcase():
encode_genotype("At")
def test_genotype__bad_input__lowercase():
encode_genotype("a")
def test_function(src, dst):
assert_equal(encode_genotype(src), dst)
def test_function(sequence):
assert_equal(encode_genotype(sequence), "Y")
def test_genotype__bad_input__unknown_nucleotide():
encode_genotype("Z")
def test_genotype__bad_input__unknown_nucleotide():
encode_genotype("Z")