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_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_disjunct(self):
from msa import Disjunct as d
self.assertEqual([x for x in d(1, 2, 3)],
[1, 2, 3])
self.assertEqual(d([1, 2, 3]),
d([1, 2, 3]))
def test_disjunct_compact_simplify(self):
from msa import Disjunct as d
self.assertEqual(d(['1', '2', ('45',), '', '3']),
d(['1', d('2', d(('4', '5'), '')), '3']).simplify().compact())
def test_disjunct_simplify_empty(self):
from msa import simplify, Disjunct as d
self.assertEqual(['1', d('2', ()), '3'],
simplify(['1', d('2', ()), '3']))
def test_disjunct_simplify_nonflat(self):
from msa import Disjunct as d
self.assertEqual(d(['1', '2', ('4', '5'), '', '3']),
d(['1', d('2', d(('4', '5'), '')), '3']).simplify())
self.assertEqual(d(['1', '2', ('4', '5'), '', '3']),
d(['1', d('2', d(('4', ('5',)), '')), '3']).simplify())
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_disjunct_compact_simplify(self):
from msa import Disjunct as d
self.assertEqual(d(["1", "2", ("45",), "", "3"]), d(["1", d("2", d(("4", "5"), "")), "3"]).simplify().compact())
def test_disjunct_simplify_empty(self):
from msa import simplify, Disjunct as d
self.assertEqual(["1", d("2", ()), "3"], simplify(["1", d("2", ()), "3"]))
def test_disjunct_simplify_nonflat(self):
from msa import Disjunct as d
self.assertEqual(d(["1", "2", ("4", "5"), "", "3"]), d(["1", d("2", d(("4", "5"), "")), "3"]).simplify())
self.assertEqual(d(["1", "2", ("4", "5"), "", "3"]), d(["1", d("2", d(("4", ("5",)), "")), "3"]).simplify())