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_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_include_gaps_from_binalign(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, include_gaps=True)
full_map = bin_align.index_map()
self.assertTrue(
np.array_equal(full_map,
[[0, 5], [5, 10], [10, 15], [15, 36], [36, 57]]))
def test_binalign_object_method_full_map(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)
full_map = bin_align.index_map()
self.assertTrue(
np.array_equal(full_map,
[[0, 4], [4, 8], [8, 12], [12, 32], [32, 52]]))
def test_multi_alpha_roundtrip(self):
from multicov.alignment import Alignment, ReferenceMapping
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)
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)
align_again = bin_align.to_alignment()
self.assertEqual(align, align_again)
def test_multi_alpha(self):
from multicov.alignment import Alignment, ReferenceMapping
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)
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)
expected1 = 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]])
# A C D E F G H I K L M N P Q R S T V W Y
expected2 = np.asmatrix([[
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
]])
self.assertSequenceEqual(bin_align.alphabets, [(rna_alphabet, 3),
(protein_alphabet, 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)