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"""Tests of the Enumeration and Alphabet objects.
Note: individual alphabets are typically in MolType and are tested there.
"""
import pickle
from unittest import TestCase
import numpy
import pytest
from numpy import unravel_index
from numpy.testing import assert_equal
from cogent3.core.alphabet import (
CharAlphabet,
Enumeration,
JointEnumeration,
_make_complement_array,
_make_translation_tables,
array,
get_array_type,
uint8,
uint16,
uint32,
uint64,
)
from cogent3.core.moltype import RNA
DnaBases = CharAlphabet("TCAG")
RnaBases = CharAlphabet("UCAG")
AminoAcids = CharAlphabet("ACDEFGHIKLMNPQRSTVWY")
class translation_table_tests(TestCase):
"""Tests of top-level translation table functions"""
def test_make_translation_tables(self):
"""_make_translation_tables should translate from chars to indices"""
a = "ucag"
itoa, atoi = _make_translation_tables(a)
s = "ggacu"
obs = s.translate(atoi)
self.assertEqual(obs, "\x03\x03\x02\x01\x00")
orig = obs.translate(itoa)
self.assertEqual(orig, s)
def test_make_complement_array(self):
"""_make_complement_array should identify complements correctly"""
complement_array = _make_complement_array(RNA.alphabet, RNA.complements)
test = "UCAG"
test_array = [RNA.alphabet.index(i) for i in test]
complements = complement_array.take(test_array)
result = "".join([RNA.alphabet[i] for i in complements])
self.assertEqual(result, "AGUC")
class get_array_type_tests(TestCase):
"""Tests of the get_array_type top-level function."""
def test_get_array_type(self):
"""get_array_type should return unsigned type that fits elements."""
self.assertEqual(get_array_type(0), uint8)
self.assertEqual(get_array_type(100), uint8)
self.assertEqual(get_array_type(255), uint8) # boundary case
self.assertEqual(get_array_type(257), uint16) # boundary case
self.assertEqual(get_array_type(10000), uint16)
self.assertEqual(get_array_type(65535), uint16)
self.assertEqual(get_array_type(65537), uint32)
self.assertEqual(get_array_type(1 + 2**32), uint64)
def test_get_array_type_fail(self):
"""get_array_type should return unsigned type that fits elements."""
with self.assertRaises(NotImplementedError):
self.assertEqual(get_array_type(2**64), uint64)
class EnumerationTests(TestCase):
"""Tests of the Enumeration object."""
def test_init(self):
"""Enumeration init should work from any sequence"""
a = Enumeration("abc")
self.assertEqual(a.index("a"), 0)
self.assertEqual(a.index("b"), 1)
self.assertEqual(a.index("c"), 2)
self.assertEqual(a[0], "a")
self.assertEqual(a[1], "b")
self.assertEqual(a[2], "c")
self.assertEqual(a.array_type, uint8)
a = Enumeration("bca")
self.assertEqual(a.index("b"), 0)
self.assertEqual(a.index("c"), 1)
self.assertEqual(a.index("a"), 2)
self.assertEqual(a[0], "b")
self.assertEqual(a[1], "c")
self.assertEqual(a[2], "a")
a = Enumeration([1, "2"])
self.assertEqual(a.index(1), 0)
self.assertEqual(a.index("2"), 1)
self.assertRaises(KeyError, a.index, "1")
# check that it works with gaps
a = Enumeration("ab-", "-")
self.assertEqual(a.gap, "-")
self.assertEqual(a.gap_index, 2)
a = Enumeration(list(range(257))) # too big to fit in uint8
self.assertEqual(a.array_type, uint16)
def test_index(self):
"""Enumeration index should return first index of item"""
a = Enumeration("bca")
self.assertEqual(a.index("b"), 0)
self.assertEqual(a.index("c"), 1)
self.assertEqual(a.index("a"), 2)
def test_getitem(self):
"""Enumeration[i] should return character at i"""
a = Enumeration("bca")
self.assertEqual(a[0], "b")
self.assertEqual(a[1], "c")
self.assertEqual(a[2], "a")
def test_to_indices(self):
"""Enumeration to_indices should return indices from elements"""
a = Enumeration("bca")
self.assertEqual(a.to_indices(""), [])
self.assertEqual(a.to_indices("ccabac"), [1, 1, 2, 0, 2, 1])
def test_is_valid(self):
"""Enumeration is_valid should return True for valid sequence"""
a = Enumeration("bca")
self.assertEqual(a.is_valid(""), True)
self.assertEqual(a.is_valid("bbb"), True)
self.assertEqual(a.is_valid("bbbaac"), True)
self.assertEqual(a.is_valid("bbd"), False)
self.assertEqual(a.is_valid("d"), False)
self.assertEqual(a.is_valid(["a", "b"]), True)
self.assertEqual(a.is_valid(["a", None]), False)
def test_from_indices(self):
"""Enumeration from_indices should return elements from indices"""
a = Enumeration("bca")
self.assertEqual(a.from_indices([]), [])
self.assertEqual(a.from_indices([1, 1, 2, 0, 2, 1]), list("ccabac"))
def test_pow(self):
"""Enumeration pow should produce JointEnumeration with n copies"""
a = AminoAcids**3
self.assertEqual(a[0], (AminoAcids[0],) * 3)
self.assertEqual(a[-1], (AminoAcids[-1],) * 3)
self.assertEqual(len(a), len(AminoAcids) ** 3)
self.assertEqual(a.array_type, uint16)
# check that it works with gaps
a = Enumeration("a-b", "-")
b = a**3
self.assertEqual(len(b), 27)
self.assertEqual(b.gap, ("-", "-", "-"))
self.assertEqual(b.gap_index, 13)
self.assertEqual(b.array_type, uint8)
# check that array type is set correctly if needed
b = a**6 # too big to fit in char
self.assertEqual(b.array_type, uint16)
def test_mul(self):
"""Enumeration mul should produce correct JointEnumeration"""
a = DnaBases * RnaBases
self.assertEqual(len(a), 16)
self.assertEqual(a[0], ("T", "U"))
self.assertEqual(a[-1], ("G", "G"))
# check that it works with gaps
a = Enumeration("ab-", "-")
b = Enumeration("xz", "z")
x = a * b
self.assertEqual(x.gap, ("-", "z"))
self.assertEqual(x.gap_index, 5)
self.assertEqual(len(x), 6)
self.assertEqual(
x, (("a", "x"), ("a", "z"), ("b", "x"), ("b", "z"), ("-", "x"), ("-", "z"))
)
# check that it doesn't work when only one seq has gaps
c = Enumeration("c")
x = a * c
self.assertEqual(x.gap, None)
class CharAlphabetTests(TestCase):
"""Tests of CharAlphabets."""
def test_init(self):
"""CharAlphabet init should make correct translation tables"""
r = CharAlphabet("UCAG")
i2c, c2i = r._indices_nums_to_chars, r._chars_to_indices
s = array([0, 0, 1, 0, 3, 2], "b").tobytes()
self.assertEqual(s.translate(i2c), b"UUCUGA")
self.assertEqual("UUCUGA".translate(c2i), "\000\000\001\000\003\002")
def test_pickling(self):
r = CharAlphabet("UCAG")
wa = r.get_word_alphabet(2)
pkl = pickle.dumps(r)
got = pickle.loads(pkl)
self.assertIsInstance(got, type(r))
self.assertEqual(got.get_word_alphabet(2), wa)
def test_pickling_moltype(self):
from cogent3.core.moltype import DNA
a = DNA.alphabet
got = pickle.loads(pickle.dumps(a))
assert got.moltype is not None
def test_word_alphabet_order(self):
bases = "TCAG"
r = CharAlphabet(bases)
indices = [unravel_index(i, shape=(4, 4, 4)) for i in range(64)]
expect = tuple("".join([bases[b] for b in coord]) for coord in indices)
got = tuple(r.get_word_alphabet(3))
assert got == expect
def test_is_valid(self):
"""CharAlphabet is_valid should return True for valid sequence"""
a = CharAlphabet("bca")
self.assertEqual(a.is_valid(""), True)
self.assertEqual(a.is_valid("bbb"), True)
self.assertEqual(a.is_valid("bbbaac"), True)
self.assertEqual(a.is_valid("bbd"), False)
self.assertEqual(a.is_valid("d"), False)
self.assertEqual(a.is_valid(["a", "b"]), True)
self.assertEqual(a.is_valid(["a", None]), False)
def test_to_chars(self):
"""CharAlphabet to_chars should convert an input array to chars"""
r = CharAlphabet("UCAG")
c = r.to_chars(array([[0, 0, 1], [0, 3, 2]], "B"))
assert_equal(c, array(["UUC", "UGA"], "c"))
def test_to_string(self):
"""CharAlphabet to_string should convert an input array to string"""
r = CharAlphabet("UCAG")
self.assertEqual(r.to_string(array([[0, 0, 1], [0, 3, 2]], "B")), "UUC\nUGA")
# should work with single seq
self.assertEqual(r.to_string(array([[0, 0, 1, 0, 3, 2]], "B")), "UUCUGA")
# should work with single seq
self.assertEqual(r.to_string(array([0, 0, 1, 0, 3, 2], "B")), "UUCUGA")
# should work with empty seq
self.assertEqual(r.to_string(array([], "B")), "")
class JointEnumerationTests(TestCase):
"""Tests of JointEnumerations."""
def test_init(self):
"""JointEnumeration init should work as expected"""
# should work for alphabet object
a = JointEnumeration([DnaBases, RnaBases])
self.assertEqual(len(a), 16)
self.assertEqual(a.shape, (4, 4))
self.assertEqual(a[0], ("T", "U"))
self.assertEqual(a[-1], ("G", "G"))
assert_equal(a._sub_enum_factors, array([[4], [1]]))
# should work for arbitrary sequences
a = JointEnumeration(["TCAG", "UCAG"])
self.assertEqual(len(a), 16)
self.assertEqual(a[0], ("T", "U"))
self.assertEqual(a[-1], ("G", "G"))
assert_equal(a._sub_enum_factors, array([[4], [1]]))
# should work for different length sequences
a = JointEnumeration(["TCA", "UCAG"])
self.assertEqual(a.shape, (3, 4))
self.assertEqual(len(a), 12)
self.assertEqual(a[0], ("T", "U"))
self.assertEqual(a[-1], ("A", "G"))
assert_equal(a._sub_enum_factors, array([[4], [1]])) # note: _not_ [3,1]
def test_to_indices(self):
"""JointEnumeration to_indices should convert tuples correctly"""
a = JointEnumeration(["TCAG", "UCAG"])
i = a.to_indices([("T", "U"), ("G", "G"), ("G", "G")])
self.assertEqual(i, [0, 15, 15])
def test_from_indices(self):
"""JointEnumeration from_indices should return correct tuples"""
a = JointEnumeration(["TCAG", "UCAG"])
i = a.from_indices([0, 15, 15])
self.assertEqual(i, [("T", "U"), ("G", "G"), ("G", "G")])
def test_pack_arrays(self):
"""JointEnumeration pack_arrays should return correct array."""
a = JointEnumeration(["xyz", "abcd", "ef"])
v = [[0, 1, 2, 0], [3, 3, 1, 0], [1, 1, 0, 0]]
result = a.pack_arrays(v)
assert_equal(result, array([7, 15, 18, 0]))
def test_unpack_arrays(self):
"""JointEnumeration unpack_arrays should return correct arrays."""
a = JointEnumeration(["xyz", "abcd", "ef"])
v = [7, 15, 18, 0]
result = a.unpack_arrays(v)
assert_equal(result, array([[0, 1, 2, 0], [3, 3, 1, 0], [1, 1, 0, 0]]))
@pytest.mark.parametrize("data", ("AUGGA", b"AUGGA"))
def test_to_indices(data):
alphabet = RNA.alphabets.degen_gapped
got = alphabet.to_indices(data)
assert got.tolist() == [2, 0, 3, 3, 2]
@pytest.mark.parametrize("cls", (list, numpy.array, tuple))
def test_from_indices(cls):
data = cls([2, 0, 3, 3, 2])
alphabet = RNA.alphabets.degen_gapped
got = alphabet.from_indices(data)
assert got == "AUGGA"
|
