def test_raise_on_empty_seq(self):
from multicov.alignment import Alignment
from multicov.alphabet import protein_alphabet
from multicov.filtering import search
align = Alignment(['IVGGYTCQ', '-VGGTEAQ', 'IGG-KDT-'],
alphabet=protein_alphabet)
with self.assertRaises(ValueError):
search(align, '')
def test_move_to_top(self):
from multicov.alignment import Alignment
from multicov.alphabet import protein_alphabet
from multicov.filtering import search
align = Alignment(['IVGGYTCQ', '-VGGTEAQ', 'IGG-KDT-'],
alphabet=protein_alphabet)
search(align, ['I', 'G', 'G', 'K', 'D', 'T'], move_to_top=True)
self.assertTrue(
np.array_equal(
align.data,
np.asmatrix([['I', 'G', 'G', '-', 'K', 'D', 'T', '-'],
['-', 'V', 'G', 'G', 'T', 'E', 'A', 'Q'],
['I', 'V', 'G', 'G', 'Y', 'T', 'C', 'Q']])))
def test_search_dna(self):
from multicov.alignment import Alignment
from multicov.alphabet import dna_alphabet
from multicov.filtering import search
align = Alignment(['ATACAT', 'GATACA', 'AA--GG'], dna_alphabet)
self.assertEqual(search(align, 'AAGG'), 2)
def test_search_approx(self):
from multicov.alignment import Alignment
from multicov.alphabet import protein_alphabet
from multicov.filtering import search
align = Alignment(['IVGGYTCQ', '-VGGTEAQ', 'IGG-KDT-'],
alphabet=protein_alphabet)
self.assertEqual(search(align, 'IGGYTCQ'), 0)
def test_search_list(self):
from multicov.alignment import Alignment
from multicov.alphabet import protein_alphabet
from multicov.filtering import search
align = Alignment(['IVGGYTCQ', '-VGGTEAQ', 'IGG-KDT-'],
alphabet=protein_alphabet)
self.assertEqual(search(align, ['I', 'G', 'G', 'K', 'D', 'T']), 2)
def test_move_to_top_but_return_old_idx(self):
from multicov.alignment import Alignment
from multicov.alphabet import protein_alphabet
from multicov.filtering import search
align = Alignment(['IVGGYTCQ', '-VGGTEAQ', 'IGG-KDT-'],
alphabet=protein_alphabet)
self.assertEqual(
search(align, ['I', 'G', 'G', 'K', 'D', 'T'], move_to_top=True), 2)
def test_raise_on_empty_align(self):
from multicov.alignment import Alignment
from multicov.filtering import search
with self.assertRaises(ValueError):
search(Alignment(), 'ABC')