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#!/usr/bin/env python
""" Unit tests for Genetic Code classes.
"""
from unittest import TestCase
import pytest
from cogent3 import DNA, RNA
from cogent3.core.genetic_code import (
DEFAULT,
GeneticCode,
GeneticCodeInitError,
GeneticCodes,
InvalidCodonError,
available_codes,
get_code,
)
class GeneticCodeTests(TestCase):
"""Tests of the GeneticCode class."""
def setUp(self):
"""Set up some standard genetic code representations."""
self.SGC = "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
self.mt = "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG"
self.AllG = "GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"
self.WrongLength = [
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG" "",
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG",
]
self.NcbiStandard = [
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
1,
"Standard",
"---M---------------M---------------M----------------------------",
]
def test_init(self):
"""GeneticCode init should work with correct-length sequences"""
sgc = GeneticCode(self.SGC)
self.assertEqual(sgc["UUU"], "F")
mt = GeneticCode(self.mt)
self.assertEqual(mt["UUU"], "F")
allg = GeneticCode(self.AllG)
self.assertEqual(allg["UUU"], "G")
for i in self.WrongLength:
self.assertRaises(GeneticCodeInitError, GeneticCode, i)
def test_standard_code(self):
"""Standard genetic code from NCBI should have correct properties"""
sgc = GeneticCode(*self.NcbiStandard)
self.assertEqual(
sgc.code_sequence,
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
)
self.assertEqual(
sgc.start_codon_sequence,
"---M---------------M---------------M----------------------------",
)
self.assertEqual(sgc.start_codons, {"TTG": "M", "CTG": "M", "ATG": "M"})
self.assertEqual(sgc.ID, 1)
self.assertEqual(sgc.name, "Standard")
self.assertEqual(sgc["UUU"], "F")
self.assertEqual(sgc.is_start("ATG"), True)
self.assertEqual(sgc.is_start("AAA"), False)
self.assertEqual(sgc.is_stop("UAA"), True)
self.assertEqual(sgc.is_stop("AAA"), False)
self.assertEqual(len(sgc.sense_codons), 61)
self.assertIn("AAA", sgc.sense_codons)
self.assertNotIn("TGA", sgc.sense_codons)
def test_standard_code_lookup(self):
"""GeneticCodes should hold codes keyed by id as string and number"""
sgc_new = GeneticCode(*self.NcbiStandard)
sgc_number = GeneticCodes[1]
sgc_string = GeneticCodes["1"]
for sgc in sgc_new, sgc_number, sgc_string:
self.assertEqual(
sgc.code_sequence,
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
)
self.assertEqual(
sgc.start_codon_sequence,
"---M---------------M---------------M----------------------------",
)
self.assertEqual(sgc.start_codons, {"TTG": "M", "CTG": "M", "ATG": "M"})
self.assertEqual(sgc.ID, 1)
self.assertEqual(sgc.name, "Standard")
self.assertEqual(sgc["TTT"], "F")
self.assertEqual(sgc.is_start("ATG"), True)
self.assertEqual(sgc.is_start("AAA"), False)
self.assertEqual(sgc.is_stop("TAA"), True)
self.assertEqual(sgc.is_stop("AAA"), False)
mtgc = GeneticCodes[2]
self.assertEqual(mtgc.name, "Vertebrate Mitochondrial")
self.assertEqual(mtgc.is_start("AUU"), True)
self.assertEqual(mtgc.is_stop("UGA"), False)
self.assertEqual(
sgc_new.changes(mtgc), {"AGA": "R*", "AGG": "R*", "ATA": "IM", "TGA": "*W"}
)
self.assertEqual(
mtgc.changes(sgc_new), {"AGA": "*R", "AGG": "*R", "ATA": "MI", "TGA": "W*"}
)
self.assertEqual(mtgc.changes(mtgc), {})
self.assertEqual(
mtgc.changes(
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
),
{"AGA": "*R", "AGG": "*R", "ATA": "MI", "TGA": "W*"},
)
def test_str(self):
"""GeneticCode str() should return its code string"""
code_strings = self.SGC, self.mt, self.AllG
codes = list(map(GeneticCode, code_strings))
for code, string in zip(codes, code_strings):
self.assertEqual(str(code), string)
# check an example directly in case strings are bad
self.assertEqual(
str(self.SGC),
"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
)
def test_cmp(self):
"""GeneticCode cmp() should act on code strings"""
sgc_1 = GeneticCode(self.SGC)
sgc_2 = GeneticCode(self.SGC)
self.assertEqual(sgc_1 is sgc_2, False) # ensure different objects
# self.assertNotEqual(sgc_1, sgc_2) # GREG
self.assertEqual(sgc_1, sgc_2)
mtgc = GeneticCode(self.mt)
self.assertNotEqual(sgc_1, mtgc)
def test_getitem_codon(self):
"""GeneticCode getitem should return amino acid for codon"""
# specific checks of a particular codon in the standard code
variant_codons = ["AUU", "AUU", "AUU", "ATT", "ATU", "ATU"]
sgc = GeneticCode(self.SGC)
for i in variant_codons:
self.assertEqual(sgc[i], "I")
# full check for the standard code
codons = [a + b + c for a in "UCAG" for b in "TCAG" for c in "UCAG"]
for codon, aa in zip(codons, self.SGC):
self.assertEqual(sgc[codon], aa)
# full check for another code
allg = GeneticCode(self.AllG)
for codon, aa in zip(codons, self.AllG):
self.assertEqual(allg[codon], aa)
# check that degenerate codon returns X
self.assertEqual(sgc["NNN"], "X")
def test_getitem_aa(self):
"""GeneticCode getitem should return codon set for aa"""
# for all G, should return all the codons (in some order)
allg = GeneticCode(self.AllG)
codons = [a + b + c for a in "TCAG" for b in "TCAG" for c in "TCAG"]
g_codons = allg["G"]
codons_copy = codons[:]
self.assertEqual(g_codons, codons_copy)
# check some known cases in the standard genetic code
sgc = GeneticCode(self.SGC)
exp_ile = ["ATT", "ATC", "ATA"]
obs_ile = sgc["I"]
self.assertEqual(obs_ile, exp_ile)
sgc["R"]
self.assertEqual(obs_ile, exp_ile)
exp_leu = ["TTA", "TTG", "CTT", "CTC", "CTA", "CTG"]
obs_leu = sgc["L"]
self.assertEqual(obs_leu, exp_leu)
exp_met = ["ATG"]
obs_met = sgc["M"]
self.assertEqual(obs_met, exp_met)
# unknown aa should return []
self.assertEqual(sgc["U"], [])
def test_getitem_invalid_length(self):
"""GeneticCode getitem should raise InvalidCodonError on wrong length"""
sgc = GeneticCode(self.SGC)
self.assertRaises(InvalidCodonError, sgc.__getitem__, "AAAA")
self.assertRaises(InvalidCodonError, sgc.__getitem__, "AA")
def test_Blocks(self):
"""GeneticCode Blocks should return correct list"""
sgc = GeneticCode(self.SGC)
exp_blocks = [
["TTT", "TTC"],
["TTA", "TTG"],
["TCT", "TCC", "TCA", "TCG"],
["TAT", "TAC"],
["TAA", "TAG"],
["TGT", "TGC"],
["TGA"],
["TGG"],
["CTT", "CTC", "CTA", "CTG"],
["CCT", "CCC", "CCA", "CCG"],
["CAT", "CAC"],
["CAA", "CAG"],
["CGT", "CGC", "CGA", "CGG"],
["ATT", "ATC"],
["ATA"],
["ATG"],
["ACT", "ACC", "ACA", "ACG"],
["AAT", "AAC"],
["AAA", "AAG"],
["AGT", "AGC"],
["AGA", "AGG"],
["GTT", "GTC", "GTA", "GTG"],
["GCT", "GCC", "GCA", "GCG"],
["GAT", "GAC"],
["GAA", "GAG"],
["GGT", "GGC", "GGA", "GGG"],
]
self.assertEqual(sgc.blocks, exp_blocks)
def test_Anticodons(self):
"""GeneticCode anticodons should return correct list"""
sgc = GeneticCode(self.SGC)
exp_anticodons = {
"F": ["AAA", "GAA"],
"L": ["TAA", "CAA", "AAG", "GAG", "TAG", "CAG"],
"Y": ["ATA", "GTA"],
"*": ["TTA", "CTA", "TCA"],
"C": ["ACA", "GCA"],
"W": ["CCA"],
"S": ["AGA", "GGA", "TGA", "CGA", "ACT", "GCT"],
"P": ["AGG", "GGG", "TGG", "CGG"],
"H": ["ATG", "GTG"],
"Q": ["TTG", "CTG"],
"R": ["ACG", "GCG", "TCG", "CCG", "TCT", "CCT"],
"I": ["AAT", "GAT", "TAT"],
"M": ["CAT"],
"T": ["AGT", "GGT", "TGT", "CGT"],
"N": ["ATT", "GTT"],
"K": ["TTT", "CTT"],
"V": ["AAC", "GAC", "TAC", "CAC"],
"A": ["AGC", "GGC", "TGC", "CGC"],
"D": ["ATC", "GTC"],
"E": ["TTC", "CTC"],
"G": ["ACC", "GCC", "TCC", "CCC"],
}
self.assertEqual(sgc.anticodons, exp_anticodons)
def test_translate(self):
"""GeneticCode translate should return correct amino acid string"""
allg = GeneticCode(self.AllG)
sgc = GeneticCode(self.SGC)
mt = GeneticCode(self.mt)
seq = "AUGCAUGACUUUUGA"
# . . . . . markers for codon start
self.assertEqual(allg.translate(seq), "GGGGG")
self.assertEqual(allg.translate(seq, 1), "GGGG")
self.assertEqual(allg.translate(seq, 2), "GGGG")
self.assertEqual(allg.translate(seq, 3), "GGGG")
self.assertEqual(allg.translate(seq, 4), "GGG")
self.assertEqual(allg.translate(seq, 12), "G")
self.assertEqual(allg.translate(seq, 14), "")
self.assertRaises(ValueError, allg.translate, seq, 15)
self.assertRaises(ValueError, allg.translate, seq, 20)
self.assertEqual(sgc.translate(seq), "MHDF*")
self.assertEqual(sgc.translate(seq, 3), "HDF*")
self.assertEqual(sgc.translate(seq, 6), "DF*")
self.assertEqual(sgc.translate(seq, 9), "F*")
self.assertEqual(sgc.translate(seq, 12), "*")
self.assertEqual(sgc.translate(seq, 14), "")
# check shortest translatable sequences
self.assertEqual(sgc.translate("AAA"), "K")
self.assertEqual(sgc.translate(""), "")
# check that different code gives different results
self.assertEqual(mt.translate(seq), "MHDFW")
# check translation with invalid codon(s)
self.assertEqual(sgc.translate("AAANNNCNC123UUU"), "KXXXF")
def test_sixframes(self):
"""GeneticCode sixframes should provide six-frame translation"""
class fake_rna(str):
"""Fake RNA class with reverse-complement"""
def __new__(cls, seq, rev):
return str.__new__(cls, seq)
def __init__(self, seq, rev):
self.seq = seq
self.rev = rev
def rc(self):
return self.rev
test_rna = fake_rna("AUGCUAACAUAAA", "UUUAUGUUAGCAU")
# . . . . . . . . . .
sgc = GeneticCode(self.SGC)
self.assertEqual(
sgc.sixframes(test_rna), ["MLT*", "C*HK", "ANI", "FMLA", "LC*H", "YVS"]
)
# should also actually work with an RNA or DNA sequence!!!
test_rna = RNA.make_seq("AUGCUAACAUAAA")
self.assertEqual(
sgc.sixframes(test_rna), ["MLT*", "C*HK", "ANI", "FMLA", "LC*H", "YVS"]
)
def test_stop_indexes(self):
"""should return stop codon indexes for a specified frame"""
sgc = GeneticCode(self.SGC)
seq = DNA.make_seq("ATGCTAACATAAA")
expected = [[9], [4], []]
for frame, expect in enumerate(expected):
got = sgc.get_stop_indices(seq, start=frame)
self.assertEqual(got, expect)
def test_Synonyms(self):
"""GeneticCode synonyms should return aa -> codon set mapping."""
expected_synonyms = {
"A": ["GCT", "GCC", "GCA", "GCG"],
"C": ["TGT", "TGC"],
"D": ["GAT", "GAC"],
"E": ["GAA", "GAG"],
"F": ["TTT", "TTC"],
"G": ["GGT", "GGC", "GGA", "GGG"],
"H": ["CAT", "CAC"],
"I": ["ATT", "ATC", "ATA"],
"K": ["AAA", "AAG"],
"L": ["TTA", "TTG", "CTT", "CTC", "CTA", "CTG"],
"M": ["ATG"],
"N": ["AAT", "AAC"],
"P": ["CCT", "CCC", "CCA", "CCG"],
"Q": ["CAA", "CAG"],
"R": ["AGA", "AGG", "CGT", "CGC", "CGA", "CGG"],
"S": ["TCT", "TCC", "TCA", "TCG", "AGT", "AGC"],
"T": ["ACT", "ACC", "ACA", "ACG"],
"V": ["GTT", "GTC", "GTA", "GTG"],
"W": ["TGG"],
"Y": ["TAT", "TAC"],
"*": ["TAA", "TAG", "TGA"],
}
obs_synonyms = GeneticCode(self.SGC).synonyms
# note that the lists will be arbitrary-order
for i in expected_synonyms:
self.assertCountEqual(obs_synonyms[i], expected_synonyms[i])
def test_get_code(self):
"""correctly return the genetic code"""
for code_id in [1, "1", "Standard", DEFAULT]:
got = get_code(code_id)
self.assertEqual(got, DEFAULT)
got = get_code(2)
self.assertEqual(got.name.lower(), "vertebrate mitochondrial")
def test_available_codes(self):
"""avaialable_codes returns Table with correct shape"""
codes = available_codes()
self.assertTrue(codes.shape[0] > 17)
self.assertEqual(codes[0, "Name"], "Standard")
def test_to_table(self):
"""tests to_table method."""
from cogent3.core.moltype import IUPAC_PROTEIN_code_aa
sgc = GeneticCode(self.SGC)
table = sgc.to_table()
# check num rows
self.assertEqual(table.shape[0], len(IUPAC_PROTEIN_code_aa))
# check there are 3 headers
self.assertEqual(table.shape[1], 3)
def test_to_regex(self):
"""creates a regex from aa seq to match a DNA sequence"""
import re
from cogent3 import make_seq
dna = "ACCGAACAGGGC"
aa = "TEQG"
pattern = DEFAULT.to_regex(aa)
self.assertTrue("".join(re.findall(pattern, dna)) == dna)
# note that Z is Q or E
aa = "TZQG"
pattern = DEFAULT.to_regex(aa)
self.assertTrue("".join(re.findall(pattern, dna)) == dna)
aa = make_seq(aa, moltype="protein")
pattern = DEFAULT.to_regex(aa)
self.assertTrue("".join(re.findall(pattern, dna)) == dna)
def test_repr_html(self):
"""exercising the _repr_html_ method"""
gc = get_code(1)
got = gc._repr_html_().strip()
self.assertTrue(
'<div class="c3table">' in got or '<div class="c3align">' in got
)
self.assertTrue("<table>" in got)
self.assertTrue("</table>" in got)
self.assertIn("Standard", got)
# starting pytest versions
@pytest.mark.parametrize("code", (1, 2))
def test_get_alphabet(code):
from cogent3.core.alphabet import Alphabet
gc = get_code()
alpha_w_stop = gc.get_alphabet(include_stop=True)
assert tuple(alpha_w_stop) == tuple(gc.codons)
assert isinstance(alpha_w_stop, Alphabet)
alpha_wo_stop = gc.get_alphabet(include_stop=False)
assert tuple(alpha_wo_stop) == tuple(gc.sense_codons)
assert isinstance(alpha_wo_stop, Alphabet)
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