115 lines
2.7 KiB
C++
115 lines
2.7 KiB
C++
/*
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* Author: Guoyi Zhang
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* Date: 07 May 2024
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* License: GPLv2
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* Function: Trim the multi-sequence-
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* alignment based on the marker
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* which `m` indicates selected
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* position.
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* */
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#include <fstream>
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#include <iostream>
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#include <string>
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#include <vector>
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// Function: check the arg
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void check_argument_count(int argc, char* argv[]) {
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if (argc != 4) {
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std::cerr
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<< "Usage: " << argv[0]
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<< " <marker_fasta_file> <input_fasta_file> <output_file>"
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<< std::endl;
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exit(1);
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}
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}
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// Function: check the file
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void check_file_exists(const std::string& file) {
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std::ifstream infile(file);
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if (!infile.good()) {
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std::cerr << "Error: file " << file << " doesn't exsit"
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<< std::endl;
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exit(1);
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}
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}
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// Function: get the positions in marker file
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std::vector<int> read_positions(const std::string& file) {
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std::ifstream infile(file);
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std::string line;
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std::vector<int> positions;
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int index = 1;
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while (std::getline(infile, line)) {
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if (line[0] != '>') {
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for (char c : line) {
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if (c == 'm' || c == 'M') {
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positions.push_back(index);
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}
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index++;
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}
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}
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}
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return positions;
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}
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// Function: trimming the sequences in input_fasta_file
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void extract_characters(const std::string& line, const std::string& file,
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const std::vector<int> positions) {
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std::ofstream outfile(file, std::ios::app);
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std::string new_line;
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for (int pos : positions) {
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if (pos <= line.length()) {
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new_line += line[pos - 1]; // start from 0
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}
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}
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for (size_t i = 0; i < new_line.length(); i += 60) {
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int num_chars =
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std::min(static_cast<int>(new_line.length() - i), 60);
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outfile << new_line.substr(i, num_chars) << std::endl;
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}
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outfile.close();
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}
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// Function: parse the fasta multi-lines format
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void process_fasta_file(const std::string& fasta_file,
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const std::string& output_file,
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const std::vector<int> positions) {
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std::ifstream infile(fasta_file);
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std::string line;
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std::string prev_line = "";
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bool prev_line_is_header = false;
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while (std::getline(infile, line)) {
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if (line[0] == '>') {
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if (!prev_line_is_header) {
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extract_characters(prev_line, output_file,
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positions);
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}
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std::ofstream outfile(output_file, std::ios::app);
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outfile << line << std::endl;
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outfile.close();
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prev_line_is_header = true;
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} else {
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if (prev_line_is_header) {
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prev_line = "";
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prev_line_is_header = false;
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}
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prev_line += line;
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}
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}
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extract_characters(prev_line, output_file, positions);
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}
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int main(int argc, char* argv[]) {
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check_argument_count(argc, argv);
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for (int i = 1; i <= 2; i++) {
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check_file_exists(argv[i]);
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}
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std::vector<int> positions = read_positions(argv[1]);
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process_fasta_file(argv[2], argv[3], positions);
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return 0;
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}
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