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# ----------------------------------------------------------------------------
# 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()
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