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#include <gtest/gtest.h>
#include <fstream>
#include <string>
#include "io/fasta/fasta.h"
#include "macros.h"
using namespace aevol;
TEST(FastaTest, SimpleFasta) {
auto file_name = std::string("./simple_fasta.fa");
auto genome = std::string("GATTACA");
auto binary_genome = genome;
std::transform(genome.cbegin(), genome.cend(), binary_genome.begin(), atcg_to_num);
std::ofstream out_file(file_name);
out_file << ">seq_42 [organism=aevol]\n" << genome << "\n";
out_file.close();
std::ifstream fasta_file(file_name);
auto [seqid, sequence, modifiers] = read_fasta_sequence(fasta_file, file_name);
EXPECT_STREQ(seqid.c_str(), "seq_42");
EXPECT_STREQ(sequence.c_str(), binary_genome.c_str());
EXPECT_EQ(modifiers.size(), 1);
EXPECT_STREQ(modifiers.at("organism").c_str(), "aevol");
}
TEST(FastaTest, FastaWithModifiers) {
auto file_name = std::string("./fasta_with_modifiers.fa");
auto genome = std::string("GATTACA");
auto binary_genome = genome;
std::transform(genome.cbegin(), genome.cend(), binary_genome.begin(), atcg_to_num);
std::ofstream out_file(file_name);
out_file << ">seq_with_mods [organism=aevol] [mod1=value1] [mod2=123]\n" << genome << "\n";
out_file.close();
std::ifstream fasta_file(file_name);
auto [seqid, sequence, modifiers] = read_fasta_sequence(fasta_file, file_name);
EXPECT_STREQ(seqid.c_str(), "seq_with_mods");
EXPECT_STREQ(sequence.c_str(), binary_genome.c_str());
// Check modifiers
EXPECT_EQ(modifiers.size(), 3);
EXPECT_STREQ(modifiers.at("organism").c_str(), "aevol");
EXPECT_STREQ(modifiers.at("mod1").c_str(), "value1");
EXPECT_STREQ(modifiers.at("mod2").c_str(), "123");
}
TEST(FastaTest, NonAevolFasta) {
auto file_name = std::string("./non_aevol_fasta.fa");
std::ofstream out_file(file_name);
out_file << ">seq_42\n" << "GATTACA\n";
out_file.close();
std::ifstream fasta_file(file_name);
EXPECT_THROW(read_fasta_sequence(fasta_file, file_name), non_aevol_fasta_error);
}
TEST(FastaTest, NonValidFasta) {
auto file_name = std::string("./non_valid_fasta.fa");
std::ofstream out_file(file_name);
out_file << "seq_42\n" << "GATTACA\n";
out_file.close();
std::ifstream fasta_file(file_name);
EXPECT_THROW(read_fasta_sequence(fasta_file, file_name), fasta_error);
}
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