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