RGBEPP/delstop.cpp

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/*
* This script is for deleting stop codon
* in both AA and original_NT files
* Copyright
* Guoyi Zhang, UNSW & Australian Museum
*/
#include <filesystem>
#include <fstream>
#include <iostream>
#include <string>
#include <unordered_map>
#include <vector>
namespace fs = std::filesystem;
class FastaProcessor {
public:
FastaProcessor(const std::string& inputFile,
const std::string& outputFile)
: input_file(inputFile), output_file(outputFile) {}
void processFile() {
// bakup input file
std::string backup_file = input_file + ".bak";
fs::copy_file(input_file, backup_file,
fs::copy_options::overwrite_existing);
std::ifstream infile(input_file);
std::ofstream outfile(input_file + ".tmp"); // temp file
std::string line;
while (std::getline(infile, line)) {
if (line[0] == '>') {
if (!sequence.empty()) {
positions_map[taxa] =
processSequence(sequence);
outfile << taxa << "\n"
<< sequence << "\n";
}
taxa = line;
sequence.clear();
} else {
sequence = line;
}
}
// process final taxa
if (!sequence.empty()) {
positions_map[taxa] = processSequence(sequence);
outfile << taxa << "\n" << sequence << "\n";
}
infile.close();
outfile.close();
// overwrite with temp file
fs::rename(input_file + ".tmp", input_file);
// process same name file
if (fs::exists(output_file)) {
// backup outputfile
std::string output_backup_file = output_file + ".bak";
fs::copy_file(output_file, output_backup_file,
fs::copy_options::overwrite_existing);
processOutputFile();
fs::rename(output_file + ".tmp", output_file);
}
}
private:
std::string input_file;
std::string output_file;
std::string taxa;
std::string sequence;
std::unordered_map<std::string, std::vector<size_t>> positions_map;
std::vector<size_t> processSequence(std::string& sequence) {
std::vector<size_t> positions;
size_t non_dash_index = 0;
for (size_t i = 0; i < sequence.size(); ++i) {
if (sequence[i] != '-') {
non_dash_index++;
if (sequence[i] == '!' || sequence[i] == '*') {
positions.push_back(
non_dash_index); // pos without -
sequence[i] = '-'; // replace with -
}
}
}
return positions;
}
void processOutputFile() {
std::ifstream infile(output_file);
std::ofstream outfile(output_file + ".tmp");
std::string line;
std::string current_taxa;
std::string current_sequence;
while (std::getline(infile, line)) {
if (line[0] == '>') {
if (!current_sequence.empty() &&
positions_map.find(current_taxa) !=
positions_map.end()) {
replacePositions(
current_sequence,
positions_map[current_taxa]);
outfile << current_taxa << "\n"
<< current_sequence << "\n";
}
current_taxa = line;
current_sequence.clear();
} else {
current_sequence = line;
}
}
// process final taxa
if (!current_sequence.empty() &&
positions_map.find(current_taxa) != positions_map.end()) {
replacePositions(current_sequence,
positions_map[current_taxa]);
outfile << current_taxa << "\n"
<< current_sequence << "\n";
}
infile.close();
outfile.close();
}
void replacePositions(std::string& sequence,
const std::vector<size_t>& positions) {
std::string new_sequence = sequence;
size_t sequence_length = sequence.size();
for (size_t pos : positions) {
size_t start = (pos * 3) - 3; // 3n-2
size_t end = pos * 3; // 3n
if (start < sequence_length) {
for (size_t i = start;
i < end && i < sequence_length; ++i) {
new_sequence[i] = '-';
}
}
}
sequence = new_sequence;
}
};
int main(int argc, char* argv[]) {
if (argc != 3) {
std::cerr << "Usage: " << argv[0]
<< " <input_folder> <output_folder>" << std::endl;
return 1;
}
std::string input_folder = argv[1];
std::string output_folder = argv[2];
// get all fasta
for (const auto& entry : fs::directory_iterator(input_folder)) {
if (entry.path().extension() == ".fasta" ||
entry.path().extension() == ".fas") {
std::string input_file = entry.path().string();
std::string output_file =
output_folder + "/" +
entry.path().filename().string();
FastaProcessor processor(input_file, output_file);
processor.processFile();
}
}
return 0;
}