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_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_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_numeric_nonzero_base_len(self):
from multicov.alphabet import NumericAlphabet
self.assertEqual(len(NumericAlphabet(11, 17)), 6)
def test_numeric_gapless_nonzero_base_size_nogap(self):
from multicov.alphabet import NumericAlphabet
self.assertEqual(NumericAlphabet(10, 16, has_gap=True).size(no_gap=True), 5)
def test_numeric_base0_len(self):
from multicov.alphabet import NumericAlphabet
self.assertEqual(len(NumericAlphabet(8)), 8)
def test_numeric_base0_force_nogap(self):
from multicov.alphabet import NumericAlphabet
self.assertFalse(NumericAlphabet(8, has_gap=False).has_gap)
def test_numeric_base0_default_gap(self):
from multicov.alphabet import NumericAlphabet
self.assertTrue(NumericAlphabet(6).has_gap)
def test_numeric_sequence_example_base0(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(10)
self.assertTrue(np.array_equal(alpha.from_int([8, 0, 4, 2]), [8, 0, 4, 2]))
def test_numeric_name_base_0(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(7)
self.assertEqual(alpha.name, 'numeric[0:7]')
def test_numeric_nonzero_base_smaller_end(self):
from multicov.alphabet import NumericAlphabet
self.assertEqual(len(NumericAlphabet(7, 5).letters()), 0)
def test_numeric_base0_nonpositive_end(self):
from multicov.alphabet import NumericAlphabet
self.assertEqual(len(NumericAlphabet(0).letters()), 0)
self.assertEqual(len(NumericAlphabet(-5).letters()), 0)
def test_numeric_letters_nogap_nonzero_base_gapful(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(5, 11, has_gap=True)
self.assertTrue(np.array_equal(alpha.letters(no_gap=True), list(range(6, 11))))
def test_numeric_letters_nonzero_base(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(2, 7)
self.assertTrue(np.array_equal(alpha.letters(), list(range(2, 7))))
def test_numeric_letters_nogap_base0_gapless(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(4, has_gap=False)
self.assertTrue(np.array_equal(alpha.letters(no_gap=True), list(range(4))))
def test_numeric_sequence_example_base0(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(7)
result = alpha.to_int([0, 2, 3])
self.assertTrue(np.array_equal(result, [0, 2, 3]))
def test_numeric_sequence_example_nonzero_base(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(3, 8)
self.assertTrue(np.array_equal(alpha.to_int([3, 7, 5]), [0, 4, 2]))
def test_index_numeric(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(4, 8)
for i, n in enumerate(alpha.letters()):
self.assertEqual(alpha[i], n)
def test_numeric_sequence_example_nonzero_base(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(5, 10)
self.assertTrue(np.array_equal(alpha.from_int([3, 0, 2, 4]), [8, 5, 7, 9]))
def test_numeric_name_nonzero_base(self):
from multicov.alphabet import NumericAlphabet
alpha = NumericAlphabet(3, 7)
self.assertEqual(alpha.name, 'numeric[3:7]')
def test_numeric_nonzero_base_default_nogap(self):
from multicov.alphabet import NumericAlphabet
self.assertFalse(NumericAlphabet(3, 6).has_gap)
def test_numeric_base0_size(self):
from multicov.alphabet import NumericAlphabet
self.assertEqual(NumericAlphabet(8).size(), 8)
def test_numeric_nonzero_base_force_gap(self):
from multicov.alphabet import NumericAlphabet
self.assertTrue(NumericAlphabet(3, 9, has_gap=True).has_gap)
def test_numeric_base0_size_nogap(self):
from multicov.alphabet import NumericAlphabet
self.assertEqual(NumericAlphabet(8).size(no_gap=True), 7)
