# ---------------------------------------------------------------------------- # Copyright (c) 2013--, scikit-bio development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE.txt, distributed with this software. # ---------------------------------------------------------------------------- from unittest import TestCase, main import numpy as np import numpy.testing as npt from skbio.sequence._alphabet import ( _encode_alphabet, _alphabet_to_hashes, _indices_in_alphabet, _indices_in_alphabet_ascii, _indices_in_observed) class TestAlphabet(TestCase): def test_encode_alphabet(self): # ascii characters alpha = 'ACGT' exp = np.array([65, 67, 71, 84], dtype=np.uint8) npt.assert_equal(_encode_alphabet(alpha), exp) npt.assert_equal(_encode_alphabet(list(alpha)), exp) npt.assert_equal(_encode_alphabet(tuple(alpha)), exp) npt.assert_equal(_encode_alphabet(np.array(list(alpha))), exp) npt.assert_equal(_encode_alphabet(np.char.encode(list(alpha))), exp) # ascii code points codes = list(map(ord, alpha)) npt.assert_equal(_encode_alphabet(codes), exp) npt.assert_equal(_encode_alphabet(np.array(codes)), exp) npt.assert_equal(_encode_alphabet(np.array(codes).astype( np.uint8)), exp) # wrong data types with self.assertRaises(TypeError): _encode_alphabet(123) with self.assertRaises(TypeError): _encode_alphabet(set(alpha)) with self.assertRaises(TypeError): _encode_alphabet([1.0, 1.5, 2.0]) with self.assertRaises(TypeError): _encode_alphabet([['a', 'b'], ['c', 'd']]) # not single characters with self.assertRaises(ValueError): _encode_alphabet(['this', 'is', 'not']) # exceed ascii range with self.assertRaises(ValueError): _encode_alphabet([100, 200, 300]) with self.assertRaises(UnicodeEncodeError): _encode_alphabet(chr(1234) + chr(5678)) with self.assertRaises(UnicodeEncodeError): _encode_alphabet([chr(1234), chr(5678)]) def test_alphabet_to_hashes(self): alpha = 'ATGCSWRYKMBVHDN' obs = _alphabet_to_hashes(alpha) exp = np.array([ 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 0, 10, 3, 13, 255, 255, 2, 12, 255, 255, 8, 255, 9, 14, 255, 255, 255, 6, 4, 1, 255, 11, 5, 255, 7, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255], dtype=np.uint8) npt.assert_equal(obs, exp) def test_indices_in_alphabet(self): seq = 'GAGCTCA' # DNA sequence without degenerate characters alpha = 'ACGTN' # DNA alphabet exp = np.array([2, 0, 2, 1, 3, 1, 0]) # indices of characters # either alphabet or sequence may be string, list/tuple, or iterator npt.assert_equal(_indices_in_alphabet(seq, alpha), exp) npt.assert_equal(_indices_in_alphabet(list(seq), list(alpha)), exp) npt.assert_equal(_indices_in_alphabet(iter(seq), iter(alpha)), exp) # alphabet is a dictionary of character : index (most performant) npt.assert_equal(_indices_in_alphabet(seq, dict(zip(alpha, range(len( alpha))))), exp) # one character is absent from alphabet seq = 'GAGRCTCA' msg = ('One or multiple characters in the sequence are absent from ' 'the alphabet.') with self.assertRaisesRegex(ValueError, msg): _indices_in_alphabet(seq, alpha) # replace absent character with wildcard obs = _indices_in_alphabet(seq, alpha, wildcard='N') exp = np.array([2, 0, 2, 4, 1, 3, 1, 0]) npt.assert_equal(obs, exp) # wildcard not in alphabet msg = 'Wildcard character "X" is not in the alphabet.' with self.assertRaisesRegex(ValueError, msg): _indices_in_alphabet(seq, alpha, wildcard='X') # amino acid seq = 'MEEPQSDPSV' alpha = 'ARNDCQEGHILKMFPSTWYVBZX' exp = np.array([12, 6, 6, 14, 5, 15, 3, 14, 15, 19]) npt.assert_equal(_indices_in_alphabet(seq, alpha), exp) # natural language seq = 'The quick brown fox jumps over the lazy dog'.split() alpha = ['dog', 'fox', 'jumps', 'the'] obs = _indices_in_alphabet(seq, alpha, wildcard='the') exp = np.array([3, 3, 3, 1, 2, 3, 3, 3, 0]) npt.assert_equal(obs, exp) # empty sequence self.assertEqual(_indices_in_alphabet('', alpha).size, 0) def test_indices_in_alphabet_ascii(self): # convert a sequence into a vector of code points seq = 'GAGCTCA' seq = np.frombuffer(seq.encode('ascii'), dtype=np.uint8) # convert an alphabet into a vector of indices alpha = 'ACGTN' idx = np.frombuffer(alpha.encode('ascii'), dtype=np.uint8) alpha = np.full(128, 255, dtype=np.uint8) alpha[idx] = np.arange(idx.size) # a typical case obs = _indices_in_alphabet_ascii(seq, alpha) exp = np.array([2, 0, 2, 1, 3, 1, 0]) npt.assert_equal(obs, exp) self.assertTrue(obs.dtype.type is np.uint8) # one character is absent seq = np.insert(seq, 3, ord('R')) msg = ('One or multiple characters in the sequence are absent from ' 'the alphabet.') with self.assertRaisesRegex(ValueError, msg): _indices_in_alphabet_ascii(seq, alpha) # replace absent character obs = _indices_in_alphabet_ascii(seq, alpha, wildcard=ord('N')) exp = np.array([2, 0, 2, 4, 1, 3, 1, 0]) npt.assert_equal(obs, exp) self.assertTrue(obs.dtype.type is np.uint8) # wildcard not in alphabet msg = 'Wildcard character "&" is not in the alphabet.' with self.assertRaisesRegex(ValueError, msg): _indices_in_alphabet_ascii(seq, alpha, wildcard=38) def test_indices_in_observed(self): # data from human TP53 protein (NP_000537.3) seqs = ('MEEPQSDPSVEPPLSQETFSDLWKLLPE', 'NNVLSPLPSQAMDDLMLSP', 'DDIEQWFTEDPGPDEAPRMPEAA') obs_idx, obs_alp = _indices_in_observed(seqs) exp_alp = np.array(tuple('ADEFGIKLMNPQRSTVW')) exp_idx = ( np.array([8, 2, 2, 10, 11, 13, 1, 10, 13, 15, 2, 10, 10, 7, 13, 11, 2, 14, 3, 13, 1, 7, 16, 6, 7, 7, 10, 2]), np.array([9, 9, 15, 7, 13, 10, 7, 10, 13, 11, 0, 8, 1, 1, 7, 8, 7, 13, 10]), np.array([1, 1, 5, 2, 11, 16, 3, 14, 2, 1, 10, 4, 10, 1, 2, 0, 10, 12, 8, 10, 2, 0, 0])) npt.assert_equal(obs_alp, exp_alp) for obs, exp in zip(obs_idx, exp_idx): npt.assert_equal(obs, exp) # reconstruct original sequences for idx, seq in zip(obs_idx, seqs): self.assertEqual(''.join(obs_alp[idx]), seq) # sequences are numbers seqs = ([1, 4, 6, 7, 8], [3, 3, 4, 1, 0], [5, 2, 5, 8, 0]) obs_idx, obs_alp = _indices_in_observed(seqs) npt.assert_equal(obs_alp, np.arange(9)) for idx, seq in zip(obs_idx, seqs): npt.assert_equal(obs_alp[idx], np.array(seq)) # sequences are natural language seqs = (['this', 'is', 'a', 'cat'], ['that', 'is', 'a', 'dog'], ['cat', 'is', 'not', 'dog']) obs_idx, obs_alp = _indices_in_observed(seqs) exp_alp = np.unique(np.concatenate(seqs)) npt.assert_equal(obs_alp, exp_alp) for idx, seq in zip(obs_idx, seqs): npt.assert_equal(obs_alp[idx], np.array(seq)) # sequences are individual characters obs_idx, obs_alp = _indices_in_observed(['hello']) npt.assert_equal(obs_alp, np.array(['e', 'h', 'l', 'o'])) self.assertEqual(''.join(obs_alp[np.concatenate(obs_idx)]), 'hello') # empty sequence obs_idx, obs_alp = _indices_in_observed([[]]) self.assertEqual(obs_alp.size, 0) self.assertEqual(len(obs_idx), 1) self.assertEqual(obs_idx[0].size, 0) if __name__ == "__main__": main()