def test_add_array_gap(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import dna_alphabet, rna_alphabet
bin_align = BinaryAlignment(
[[0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0]],
dna_alphabet,
include_gaps=True)
bin_align.add(
[[0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0]],
rna_alphabet)
self.assertSequenceEqual(bin_align.alphabets, [(dna_alphabet, 4),
(rna_alphabet, 4)])
self.assertTrue(
np.array_equal(
bin_align.data.todense(),
np.asmatrix([[
0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1
],
[
0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 1
],
[
0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0,
1, 0, 0, 0, 0, 0, 1, 0, 0, 0
]])))
def test_copy(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import dna_alphabet
bin_align1 = BinaryAlignment(
[[1, 0, 0, 0, 1, 0, 0, 0], [0, 0, 0, 1, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 1, 0], [0, 0, 0, 1, 0, 0, 0, 1]], dna_alphabet)
bin_align2 = BinaryAlignment(bin_align1)
self.assertIsNot(bin_align1, bin_align2)
self.assertEqual(bin_align1, bin_align2)
def test_set_default_reference_on_empty(self):
from multicov.binary import BinaryAlignment
from multicov.alignment import ReferenceMapping
from multicov.alphabet import rna_alphabet
bin_align = BinaryAlignment()
bin_align.add([[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]],
rna_alphabet)
self.assertEqual(bin_align.reference, ReferenceMapping(list(range(4))))
def test_deep_copy_data(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import NumericAlphabet
bin_align1 = BinaryAlignment(
[[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]],
NumericAlphabet(5))
bin_align2 = BinaryAlignment(bin_align1)
self.assertIsNot(bin_align1.data, bin_align2.data)
def test_add_to_empty(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import dna_alphabet
bin_align1 = BinaryAlignment(
[[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]], dna_alphabet)
bin_align2 = BinaryAlignment()
bin_align2.add(bin_align1)
self.assertEqual(bin_align1, bin_align2)
def test_unequal_different_alphabets(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import rna_alphabet, dna_alphabet
bin_data = [[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]]
bin_align1 = BinaryAlignment(bin_data, dna_alphabet)
bin_align2 = BinaryAlignment(bin_data, rna_alphabet)
self.assertFalse(bin_align1 == bin_align2)
self.assertTrue(bin_align1 != bin_align2)
def test_exclude_gaps(self):
from multicov.alignment import Alignment
from multicov.binary import BinaryAlignment
from multicov.alphabet import rna_alphabet
align = Alignment(['ACA', 'GUA', '-A-'], alphabet=rna_alphabet)
bin_align1 = BinaryAlignment.from_alignment(align)
bin_align2 = BinaryAlignment.from_alignment(align, include_gaps=True)
bin_align2.remove_gap_positions()
self.assertEqual(bin_align1, bin_align2)
def test_rna_example(self):
from multicov.alignment import Alignment
from multicov.binary import BinaryAlignment
from multicov.alphabet import rna_alphabet
align = Alignment(['ACA', 'GUA', '-A-'], alphabet=rna_alphabet)
bin_align = BinaryAlignment.from_alignment(align)
expected = BinaryAlignment([[1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0],
[0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0]],
rna_alphabet)
self.assertEqual(bin_align, expected)
def test_equal_self_multi_alpha(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import rna_alphabet, dna_alphabet
bin_align = BinaryAlignment(
[[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]], dna_alphabet)
bin_align.add([[0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0]],
rna_alphabet)
self.assertTrue(bin_align == bin_align)
self.assertFalse(bin_align != bin_align)
def test_return_self(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import dna_alphabet, rna_alphabet
bin_align = BinaryAlignment(
[[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1],
[1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]], dna_alphabet)
ret_align = bin_align.add(
[[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1],
[1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]], rna_alphabet)
self.assertIs(bin_align, ret_align)
def test_include_gaps(self):
from multicov.alignment import Alignment, ReferenceMapping
from multicov.alphabet import rna_alphabet, NumericAlphabet
from multicov.binary import BinaryAlignment
align1 = Alignment(['ACA', 'GUA', '-A-'], alphabet=rna_alphabet)
align2 = Alignment([[2, 3], [0, 4], [1, 3]],
alphabet=NumericAlphabet(5, has_gap=False))
align = Alignment(align1).add(align2)
align.reference = ReferenceMapping((list(range(1, 4)), list(range(2))))
align.annotations['seqw'] = [0.5, 1.5, 0.2]
bin_align = BinaryAlignment.from_alignment(align)
bin_align.add_gap_positions()
expected1 = np.asmatrix([[0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0],
[1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0,
0]])
# 0 1 2 3 4
expected2 = np.asmatrix([[0, 0, 1, 0, 0, 0, 0, 0, 1, 0],
[1, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 0, 0, 0, 1, 0]])
self.assertTrue(bin_align.include_gaps)
self.assertSequenceEqual(bin_align.alphabets,
[(rna_alphabet, 3),
(NumericAlphabet(5, has_gap=False), 2)])
self.assertTrue(
np.array_equal(bin_align.data.todense(),
np.hstack((expected1, expected2))))
self.assertIs(bin_align.reference, align.reference)
self.assertIs(bin_align.annotations, align.annotations)
def test_nonempty(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import dna_alphabet
bin_align = BinaryAlignment(
[[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]], dna_alphabet)
self.assertEqual(len(bin_align), 2)
def test_get_str_goes_to_annotations(self):
from multicov.alignment import Alignment
from multicov.binary import BinaryAlignment
from multicov.alphabet import rna_alphabet
align = Alignment(['ACA', 'GUA', '-A-'], alphabet=rna_alphabet)
bin_align = BinaryAlignment.from_alignment(align)
self.assertIs(bin_align['seqw'], bin_align.annotations['seqw'])
def test_rna_roundtrip(self):
from multicov.alignment import Alignment
from multicov.binary import BinaryAlignment
from multicov.alphabet import rna_alphabet
align = Alignment(['ACA', 'GUA', '-A-'], alphabet=rna_alphabet)
bin_align = BinaryAlignment.from_alignment(align)
align_again = bin_align.to_alignment()
self.assertEqual(align, align_again)
def test_single_alpha_full_map(self):
from multicov.alignment import Alignment
from multicov.binary import BinaryAlignment, binary_index_map
from multicov.alphabet import rna_alphabet
align = Alignment(['ACA', 'GUA', '-A-'], alphabet=rna_alphabet)
bin_align = BinaryAlignment.from_alignment(align)
full_map = binary_index_map(bin_align)
self.assertTrue(np.array_equal(full_map, [[0, 4], [4, 8], [8, 12]]))
def test_copy_alpha_refmap_and_annotations_by_ref(self):
from multicov.alignment import Alignment
from multicov.binary import BinaryAlignment
from multicov.alphabet import rna_alphabet
align = Alignment(['ACA', 'GUA', '-A-'], alphabet=rna_alphabet)
bin_align = BinaryAlignment.from_alignment(align)
self.assertIs(bin_align.alphabets, align.alphabets)
self.assertIs(bin_align.reference, align.reference)
self.assertIs(bin_align.annotations, align.annotations)
def test_initially_one(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import dna_alphabet
bin_align = BinaryAlignment(
[[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1],
[1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]], dna_alphabet)
# noinspection PyTypeChecker
self.assertTrue(np.all(bin_align.annotations['seqw'] == 1))
def test_single_alpha_single_idx(self):
from multicov.alignment import Alignment
from multicov.binary import BinaryAlignment, binary_index_map
from multicov.alphabet import rna_alphabet
align = Alignment(['ACA', 'GUA', '-A-'], alphabet=rna_alphabet)
bin_align = BinaryAlignment.from_alignment(align)
self.assertSequenceEqual(binary_index_map(bin_align, 0), (0, 4))
self.assertSequenceEqual(binary_index_map(bin_align, 1), (4, 8))
self.assertSequenceEqual(binary_index_map(bin_align, 2), (8, 12))
def test_empty_vs_not(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import protein_alphabet
bin_align = BinaryAlignment(
[[
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
]], protein_alphabet)
self.assertFalse(BinaryAlignment() == bin_align)
self.assertTrue(BinaryAlignment() != bin_align)
def test_set_default_reference(self):
from multicov.binary import BinaryAlignment
from multicov.alignment import ReferenceMapping
from multicov.alphabet import NumericAlphabet
bin_align = BinaryAlignment(
[[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]],
NumericAlphabet(5))
self.assertEqual(bin_align.reference, ReferenceMapping(list(range(4))))
def test_make_empty(self):
from multicov.binary import BinaryAlignment
bin_align = BinaryAlignment()
self.assertTrue(hasattr(bin_align, 'alphabets'))
self.assertTrue(hasattr(bin_align, 'data'))
self.assertTrue(hasattr(bin_align, 'reference'))
self.assertTrue(hasattr(bin_align, 'annotations'))
self.assertEqual(np.size(bin_align.data), 0)
self.assertEqual(len(bin_align.alphabets), 0)
self.assertEqual(len(bin_align.reference), 0)
self.assertEqual(bin_align.include_gaps, False)
def test_raise_on_add_wrong_length(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import protein_alphabet, rna_alphabet
bin_align = BinaryAlignment(
[[
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
]], protein_alphabet)
with self.assertRaises(ValueError):
bin_align.add([[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]],
rna_alphabet)
def test_empty(self):
from multicov.alignment import Alignment, ReferenceMapping
from multicov.binary import BinaryAlignment
bin_align = BinaryAlignment.from_alignment(Alignment())
self.assertTrue(hasattr(bin_align, 'data'))
self.assertTrue(hasattr(bin_align, 'alphabets'))
self.assertTrue(hasattr(bin_align, 'reference'))
self.assertTrue(hasattr(bin_align, 'annotations'))
self.assertEqual(np.size(bin_align.data), 0)
self.assertEqual(np.size(bin_align.alphabets), 0)
self.assertEqual(bin_align.annotations.size, 0)
self.assertEqual(bin_align.reference, ReferenceMapping())
def test_changing_copy_leaves_original_unchanged(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import protein_alphabet
bin_align1 = BinaryAlignment(
[[
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
]], protein_alphabet)
bin_align2 = BinaryAlignment(bin_align1)
bin_align2.annotations['seqw'] = [1, 2, 3]
self.assertNotEqual(bin_align1, bin_align2)
self.assertTrue(
np.array_equal(bin_align2.annotations['seqw'], [1, 2, 3]))
def test_binalign_object_method(self):
from multicov.alignment import Alignment
from multicov.alphabet import protein_alphabet, rna_alphabet
from multicov.binary import BinaryAlignment
align1 = Alignment(['ACA', 'GUA', '-A-'], alphabet=rna_alphabet)
align2 = Alignment(['DF', 'YA', '-C'], alphabet=protein_alphabet)
align = Alignment(align1).add(align2)
bin_align = BinaryAlignment.from_alignment(align)
self.assertSequenceEqual(bin_align.index_map(2), (8, 12))
self.assertSequenceEqual(bin_align.index_map(3), (12, 32))
def test_raise_on_add_wrong_width(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import protein_alphabet, rna_alphabet
bin_align = BinaryAlignment(
[[
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
]], protein_alphabet)
data = np.asmatrix([[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]])
# don't raise on properly-sized data
try:
bin_align.add(data, rna_alphabet)
except ValueError:
self.fail(
"BinaryAlignment.add() raised ValueError on properly-sized data."
)
# raised on improperly-sized
with self.assertRaises(ValueError):
bin_align.add(data[:, :-1], rna_alphabet)
def test_set_default_reference_on_nonempty(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import protein_alphabet, dna_alphabet
bin_align = BinaryAlignment(
[[
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
]], protein_alphabet)
bin_align.add([[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1],
[1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]],
dna_alphabet)
self.assertEqual(len(bin_align.reference.seqs), 2)
self.assertSequenceEqual(bin_align.reference.seqs[1], list(range(4)))
def test_make_from_matrix(self):
from multicov.binary import BinaryAlignment
from multicov.alignment import ReferenceMapping
from multicov.alphabet import rna_alphabet
bin_data = np.asmatrix([[1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0],
[0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0]])
bin_align = BinaryAlignment(bin_data, rna_alphabet)
self.assertEqual(len(bin_align.alphabets), 1)
self.assertEqual(bin_align.alphabets[0][0], rna_alphabet)
self.assertEqual(bin_align.alphabets[0][1], 3)
self.assertEqual(bin_align.reference, ReferenceMapping(list(range(3))))
self.assertTrue(np.array_equal(bin_align.data.todense(), bin_data))
self.assertEqual(bin_align.include_gaps, False)
def test_unequal_different_annotations(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import dna_alphabet, rna_alphabet
bin_align1 = BinaryAlignment(
[[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]], dna_alphabet)
bin_align1.add([[0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0]],
rna_alphabet)
bin_align2 = BinaryAlignment(bin_align1)
bin_align2.annotations['seqw'] = [0.5, 1.2]
bin_align2.annotations['fitness'] = [0, -1]
self.assertTrue(bin_align1 != bin_align2)
self.assertFalse(bin_align1 == bin_align2)
def test_multi(self):
from multicov.binary import BinaryAlignment
from multicov.alphabet import protein_alphabet, dna_alphabet
bin_align = BinaryAlignment(
[[
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
[
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
]], protein_alphabet)
bin_align.add([[0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1],
[1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]],
dna_alphabet)
self.assertEqual(len(bin_align.alphabets), 2)
self.assertEqual(bin_align.alphabets[0], (protein_alphabet, 2))
self.assertEqual(bin_align.alphabets[1], (dna_alphabet, 4))
