def test_raises_if_first_kmer_cannot_be_connected_to_second_kmer(self):
# given
builder = EmptyKmerBuilder(1)
kmer1 = builder.build_or_get('AAA')
kmer2 = builder.build_or_get('ACC')
# when/then
with pytest.raises(ValueError):
connect_kmers(kmer1, kmer2, 0)
def test_raises_if_equal_kmers_are_not_the_same_object(self):
# given
kmer1 = EmptyKmerBuilder(1).build_or_get('AAA')
kmer2 = EmptyKmerBuilder(1).build_or_get('AAA')
assert kmer1 is not kmer2
# when/then
with pytest.raises(ValueError):
connect_kmers(kmer1, kmer2, 0)
def test_connects_kmer_to_itself(self):
# given
kmer = EmptyKmerBuilder(1).build_or_get('AAA')
# when
connect_kmers(kmer, kmer, 0)
# then
assert kmer.edges[0].is_edge('a')
assert kmer.edges[0].is_edge('A')
def test_connects_kmer_to_itself_for_one_sided_connection(self):
# given
kmer = EmptyKmerBuilder(1).build_or_get('TAA')
# when
connect_kmers(kmer, kmer, 0)
# then
assert kmer.edges[0].is_edge('t')
for letter in 'acgACGT':
assert not kmer.edges[0].is_edge(letter)
def test_works_on_edit_distance_one_forward_in_any_order(
self, data, letter, num_colors, add_letter_to_end,
add_letter_to_revcomp):
# given
builder = EmptyKmerBuilder(num_colors)
kmer1 = builder.build_or_get(data.draw(kmer_strings()))
assert kmer1.kmer < reverse_complement(kmer1.kmer)
if add_letter_to_revcomp:
kmer1_string = reverse_complement(kmer1.kmer)
else:
kmer1_string = kmer1.kmer
if add_letter_to_end:
kmer2_string = kmer1_string[1:] + letter
else:
kmer2_string = letter + kmer1_string[:-1]
kmer2 = builder.build_or_get(kmer2_string)
if add_letter_to_revcomp:
kmer1_edge_letter = reverse_complement(letter)
else:
kmer1_edge_letter = letter.lower()
if add_letter_to_end:
kmer1_edge_letter = kmer1_edge_letter.swapcase()
kmer2_edge_letter = kmer1_string[0].lower()
else:
kmer2_edge_letter = kmer1_string[-1]
if reverse_complement(kmer2_string) < kmer2_string:
kmer2_edge_letter = reverse_complement(
kmer2_edge_letter).swapcase()
for color in range(num_colors):
# when
connect_kmers(kmer1, kmer2, color)
# then
assert kmer1.edges[color].is_edge(kmer1_edge_letter)
assert kmer2.edges[color].is_edge(kmer2_edge_letter)
# let's also test connected check
if not add_letter_to_revcomp == add_letter_to_end:
assert kmer1.has_outgoing_edge_to_kmer_in_color(kmer2, color)
else:
assert kmer1.has_incoming_edge_from_kmer_in_color(kmer2, color)
# and let's check disconnect kmers
disconnect_kmers(kmer1, kmer2, [color])
assert not kmer1.edges[color].is_edge(kmer1_edge_letter)
assert not kmer2.edges[color].is_edge(kmer2_edge_letter)
def test_aag_act_connection(self):
# given
builder = EmptyKmerBuilder(1)
kmer1 = builder.build_or_get('AAG')
kmer2 = builder.build_or_get('ACT')
# when
connect_kmers(kmer1, kmer2, 0)
# then
assert kmer1.edges[0].is_edge('T')
assert kmer2.edges[0].is_edge('T')