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// ****************************************************************************
//
// Aevol - An in silico experimental evolution platform
//
// ****************************************************************************
//
// Copyright: See the AUTHORS file provided with the package or <www.aevol.fr>
// Web: http://www.aevol.fr/
// E-mail: See <http://www.aevol.fr/contact/>
// Original Authors : Guillaume Beslon, Carole Knibbe, David Parsons
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 2 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
//
//*****************************************************************************
// =================================================================
// Includes
// =================================================================
#include <gtest/gtest.h>
#include <array>
#include <memory>
#include <string>
#include <sstream>
#include "Dna.h"
#include "Individual.h"
#include "macros.h"
#include "Strand.h"
using namespace aevol;
//############################################################################
// #
// Class IndividualTest #
// #
//############################################################################
class DnaTest : public testing::Test
{
protected:
virtual void SetUp(void);
virtual void TearDown(void);
std::vector<std::string> genomes;
std::vector<std::unique_ptr<Individual>> indivs;
};
// ===========================================================================
// Public Methods
// ===========================================================================
void DnaTest::SetUp(void) {
// Build ad-hoc dna
//
// AS = Arbitrary Sequence
// AG = Arbitrary Gene
// Do not modify the sequences !
// Define arbitrary sequences
std::array<std::string, 5> as = {
"0011",
"11101",
"110011",
"11000",
"000101"
};
// Define an arbitrary gene
std::string gene = std::string(SHINE_DAL_SEQ) + "0011000100110110010001"; // S-D SPACER START M0 H0 H0 W0 STOP
// Define an arbitrary terminator
std::string term = "01000001101";
// Define a few arbitrary promoters
std::array<std::string, 2> prom = {
"0101010001110110010110", // dist from consensus: 2 => basal level: 0.6
"0101011001110010010010" // dist from consensus: 1 => basal level: 0.8
};
// Build genomes
// 0-------4---------26------31-----59------65-----76------81--------103 (total size: 109)
genomes.push_back(as[0] + prom[0] + as[1] + gene + as[2] + term + as[3] + prom[1] + as[4]);
for (const auto& genome : genomes) {
indivs.push_back(Individual::make_from_sequence(genome));
}
}
void DnaTest::TearDown() {
indivs.clear();
genomes.clear();
}
TEST_F(DnaTest, TestDna) {
// Check genome size
EXPECT_EQ(genomes[0].size(), 109);
EXPECT_EQ(genomes[0].size(), indivs[0]->dna().length());
}
TEST_F(DnaTest, TestProteins) {
auto i = 0;
indivs[i]->locate_promoters();
indivs[i]->prom_compute_RNA();
indivs[i]->start_protein();
indivs[i]->compute_protein();
indivs[i]->translate_protein(0.1);
const auto& proteins = indivs[i]->proteins();
EXPECT_EQ(proteins.size(), 2);
auto prot_it = proteins.begin();
auto prot = *prot_it;
EXPECT_EQ(prot->position_first_aa(), 44);
EXPECT_EQ(prot->is_duplicate(), false);
EXPECT_EQ(prot->size(), 4);
++prot_it;
prot = *prot_it;
EXPECT_EQ(prot->position_first_aa(), 44);
EXPECT_EQ(prot->is_duplicate(), true);
}
struct subseq_test_params {
Strand strand;
size_t first;
size_t count;
bool spans_oriC = false;
};
std::ostream& operator<<(std::ostream& os, const subseq_test_params& o) {
os << "strand: " << o.strand << " ; first: " << o.first << " ; count: " << o.count << " ; spans_oriC: "
<< (o.spans_oriC ? "true" : "false");
return os;
}
TEST_F(DnaTest, Test_subseq) {
std::array<subseq_test_params, 4> tests_leading = {{
{Strand::LEADING, 0, 10, false},
{Strand::LEADING, 10, 42, false},
{Strand::LEADING, 100, 42, true},
{Strand::LEADING, 100, genomes[0].size(), true} // Whole genome
}};
for (const auto& test : tests_leading) {
auto subseq = indivs[0]->dna().subseq(test.first, test.count, test.strand);
// Check subseq size
EXPECT_EQ(test.count, subseq.size());
// Check subseq content
if (test.spans_oriC) {
auto expected_subseq = genomes[0].substr(test.first);
expected_subseq += genomes[0].substr(0, test.count - expected_subseq.size());
EXPECT_EQ(expected_subseq, subseq)
<< "\tNote: testing (" << test << ')';
} else {
EXPECT_EQ(genomes[0].substr(test.first, test.count), subseq)
<< "\tNote: testing (" << test << ')';
}
}
std::array<subseq_test_params, 3> tests_lagging = {{
{Strand::LAGGING, 15, 12, false},
{Strand::LAGGING, genomes[0].size() - 1, genomes[0].size(), false}, // Whole genome
{Strand::LAGGING, 4, 11, true}
}};
for (const auto& test : tests_lagging) {
auto subseq = indivs[0]->dna().subseq(test.first, test.count, test.strand);
// Construct expected result (naïve mode)
std::string expected_subseq(test.count, '0');
if (test.spans_oriC) {
for (size_t i = 0; i < test.first + 1; ++i) {
expected_subseq[i] = genomes[0][test.first - i] == '0' ? '1' : '0';
}
for (size_t i = 1; i < test.count - test.first; ++i) {
expected_subseq[test.first + i] = genomes[0][genomes[0].size() - i] == '0' ? '1' : '0';
}
} else {
for (size_t i = 0 ; i < test.count ; ++i) {
expected_subseq[i] = genomes[0][test.first - i] == '0' ? '1' : '0';
}
}
EXPECT_EQ(expected_subseq, subseq)
<< "\tNote: testing (" << test << ')';
}
}
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