def test_with_reverse_and_forward_link_returns_one_base_each(self, kmer):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 1 1 A', 'AAA')
b.with_link_for_kmer('R 1 1 A', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links).load_kmer(kmer)
# then
assert ['A'] == list(walker.next_junction_bases())
def test_raises_when_base_that_does_not_exist_is_chosen(self):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 1 1 A', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links).load_kmer('AAA')
# then
with pytest.raises(KeyError):
walker.choose_branch('C')
def test_with_single_link_returns_each_junctions_base(self):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 3 1 ACT', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links).load_kmer('AAA')
# then
assert ['A'] == list(walker.next_junction_bases())
assert ['C'] == list(walker.choose_branch('A').next_junction_bases())
assert ['T'] == list(walker.choose_branch('C').next_junction_bases())
assert [] == list(walker.choose_branch('T').next_junction_bases())
def test_with_single_link_returns_one_base(self, is_lexlo):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 3 1 ACC', 'AAA')
# when
links = b.build()
# then
junctions = list(
links.body['AAA'].get_link_junctions_in_kmer_orientation(is_lexlo))
if is_lexlo:
assert ['ACC'] == junctions
else:
assert [] == junctions
def test_with_two_reverse_and_forward_links_returns_two_bases_each(self):
# given
b = LinksBuilder()
b.with_link_for_kmer('F 1 1 A', 'AAA')
b.with_link_for_kmer('F 1 1 C', 'AAA')
b.with_link_for_kmer('R 1 1 G', 'AAA')
b.with_link_for_kmer('R 1 1 T', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links)
# then
assert ['A',
'C'] == list(walker.load_kmer('AAA').next_junction_bases())
assert ['G', 'T'] == list(
walker.clear().load_kmer('TTT').next_junction_bases())
def test_with_single_reverse_link_returns_one_base(self, kmer):
# given
b = LinksBuilder()
b.with_link_for_kmer('R 3 1 GTT', 'AAA')
links = b.build()
# when
walker = LinkWalker.from_links(links).load_kmer(kmer)
# then
if kmer == 'TTT':
assert 1 == walker.n_junctions
assert ['G'] == list(walker.next_junction_bases())
walker.choose_branch('G')
assert 1 == walker.n_junctions
walker.choose_branch('T')
assert 1 == walker.n_junctions
walker.choose_branch('T')
assert 0 == walker.n_junctions
else:
assert 0 == walker.n_junctions
assert [] == list(walker.next_junction_bases())