def test_invalid_spacing():
"""
Check if expected exceptions are raised if an invalid spacing is
given.
"""
alphabet = seq.ProteinSequence.alphabet
with pytest.raises(ValueError):
# Not enough informative positions for given k
align.KmerAlphabet(alphabet, 5, spacing=[0, 1, 3, 4])
with pytest.raises(ValueError):
# Duplicate positions
align.KmerAlphabet(alphabet, 5, spacing=[0, 1, 1, 3, 4])
with pytest.raises(ValueError):
# Negative values
align.KmerAlphabet(alphabet, 5, spacing=[-1, 1, 2, 3, 4])
def test_from_sequences(k, random_sequences, spacing):
"""
Test the :meth:`from_sequences()` constructor, by checking for each
sequence position, if the position is in the C-array of the
corresponding k-mer.
"""
table = align.KmerTable.from_sequences(k,
random_sequences,
spacing=spacing)
kmer_alph = align.KmerAlphabet(random_sequences[0].alphabet, k, spacing)
assert kmer_alph == table.kmer_alphabet
for i, sequence in enumerate(random_sequences):
for j in range(kmer_alph.kmer_array_length(len(sequence))):
if spacing is None:
kmer = kmer_alph.fuse(sequence.code[j:j + k])
else:
kmer = kmer_alph.fuse(sequence.code[kmer_alph.spacing + j])
assert np.array([i, j]) in table[kmer]
def test_get_kmers():
"""
Test whether the correct used *k-mers* are returned by
:meth:`get_kmer()`, by constructing a table with exactly one
appearance for each *k-mer* in a random list of *k-mers*.
"""
np.random.seed(0)
kmer_alphabet = align.KmerAlphabet(
seq.NucleotideSequence.unambiguous_alphabet(), 8)
ref_mask = np.random.choice([False, True], size=len(kmer_alphabet))
ref_kmers = np.where(ref_mask)[0]
kmer_dict = {kmer: np.zeros((1, 2), dtype=np.uint32) for kmer in ref_kmers}
# [[0, 0]] = Dummy position
# The actual position is not relevant for the tested function
table = align.KmerTable.from_positions(kmer_alphabet, kmer_dict)
test_kmers = table.get_kmers()
assert test_kmers.tolist() == ref_kmers.tolist()
def kmer_alphabet():
return align.KmerAlphabet(seq.ProteinSequence.alphabet, 3)
def spaced_kmer_alphabet():
return align.KmerAlphabet(seq.ProteinSequence.alphabet,
K,
spacing=[0, 1, 2])