RGBEPP/splitfasta.cpp

85 lines
1.8 KiB
C++

// #include <sys/stat.h>
#include <filesystem>
#include <fstream>
#include <iostream>
// #include <sstream>
#include <string>
// #include <vector>
namespace fs = std::filesystem;
std::string removeExtension(const std::string& filename) {
size_t lastdot = filename.find_last_of(".");
if (lastdot != std::string::npos) {
return filename.substr(0, lastdot);
}
return filename;
}
void splitFasta(const std::string& input_fasta) {
std::ifstream infile(input_fasta);
if (!infile) {
std::cerr << "Error: Unable to open input file " << input_fasta
<< std::endl;
return;
}
std::string line;
std::string dir_name;
std::ofstream outfile;
bool in_sequence = false;
while (std::getline(infile, line)) {
if (line.empty()) continue;
if (line[0] == '>') {
// New sequence header
if (in_sequence) { // if found new sequence, close
outfile.close(); // previous output file
}
dir_name = line.substr(1); // Remove '>'
// directory
fs::create_directories(dir_name);
fs::path output_file =
fs::path(dir_name) /
input_fasta; // suitable to many os
outfile.open(output_file);
outfile << ">" << removeExtension(input_fasta)
<< std::endl;
// will enter sequence
in_sequence = true;
} else if (in_sequence) {
// Inside sequence content
outfile << line << std::endl;
}
}
if (in_sequence) {
outfile.close();
}
if (infile.eof()) {
std::cout << "Sequences have been split into individual files."
<< std::endl;
} else {
std::cerr << "Error occurred while reading file." << std::endl;
}
infile.close();
}
int main(int argc, char* argv[]) {
if (argc != 2) {
std::cerr << "splitFasta\nAuthor: Guoyi "
"Zhang\nLicense:GPL-2.0-only\nUsage: "
"Usage: "
<< argv[0] << " <input_fasta>" << std::endl;
return 1;
}
splitFasta(argv[1]);
return 0;
}