83 lines
1.7 KiB
C++
83 lines
1.7 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 << "Usage: " << argv[0] << " <input_fasta>"
|
|
<< std::endl;
|
|
return 1;
|
|
}
|
|
|
|
splitFasta(argv[1]);
|
|
|
|
return 0;
|
|
}
|
|
|