def test_triple_compact(self):
from msa import Disjunct as d, Sub as s
self.assertEqual(
msa.compact(msa.msa(["ABC", "BCD", "BCX"])),
[d((d((s("A"),), ()),), ()), s("BC"), d((d((), (s("D"),)),), (s("X"),))],
)
def test_edges(self):
from msa import to_edges, Edge, Disjunct as d, Sub as s
def new_edge(f, t):
return Edge(f.seq, t.seq, f.id(), t.id())
self.assertEqual(set([x for x in to_edges([d(s('A'), (s('B'), d(s('C'), s('D')))), s('E')])]),
set([
new_edge(s('START'), s('A')),
new_edge(s('START'), s('B')),
new_edge(s('B'), s('C')),
new_edge(s('B'), s('D')),
new_edge(s('E'), s('END')),
new_edge(s('C'), s('E')),
new_edge(s('D'), s('E')),
new_edge(s('A'), s('E')),
]))
def test_triple_compact(self):
from msa import Disjunct as d, Sub as s
self.assertEqual(msa.compact(msa.msa(['ABC', 'BCD', 'BCX'])),
[d((d((s('A'),), ()),), ()),
s('BC'),
d((d((), (s('D'),)),), (s('X'),))])
def test_pair(self):
from msa import Disjunct as d, Sub as s
self.assertEqual(msa.msa(['ABC', 'BCDE']),
[d((s('A'),), ()),
s('B'), s('C'),
d((), (s('D'), s('E')))])
def test_edges(self):
from msa import to_edges, Edge, Disjunct as d, Sub as s
def new_edge(f, t):
return Edge(f.seq, t.seq, f.id(), t.id())
self.assertEqual(
set([x for x in to_edges([d(s("A"), (s("B"), d(s("C"), s("D")))), s("E")])]),
set(
[
new_edge(s("START"), s("A")),
new_edge(s("START"), s("B")),
new_edge(s("B"), s("C")),
new_edge(s("B"), s("D")),
new_edge(s("E"), s("END")),
new_edge(s("C"), s("E")),
new_edge(s("D"), s("E")),
new_edge(s("A"), s("E")),
]
),
)
def test_pair(self):
from msa import Disjunct as d, Sub as s
self.assertEqual(msa.msa(["ABC", "BCDE"]), [d((s("A"),), ()), s("B"), s("C"), d((), (s("D"), s("E")))])
