89 lines
1.9 KiB
C++
89 lines
1.9 KiB
C++
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/*
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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: Generate fasta file which `m`
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* means selected position by Gblocks
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* from Gblocks html report file.
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* */
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#include <fstream>
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#include <iostream>
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#include <regex>
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#include <string>
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bool checkArguments(int argc, char* argv[]) {
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if (argc != 3) {
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std::cerr << "Usage: " << argv[0]
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<< " input_file output_file\n";
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return false;
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}
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return true;
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}
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bool openFiles(std::ifstream& input, std::ofstream& output,
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const std::string& inputFilename,
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const std::string& outputFilename) {
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input.open(inputFilename);
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if (!input.is_open()) {
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std::cerr << "Unable to open input file: " << inputFilename
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<< std::endl;
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return false;
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}
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output.open(outputFilename);
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if (!output.is_open()) {
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std::cerr << "Unable to open output file: " << outputFilename
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<< std::endl;
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input.close();
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return false;
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}
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return true;
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}
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void closeFiles(std::ifstream& input, std::ofstream& output) {
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input.close();
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output.close();
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}
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void processFile(const std::string& inputFilename,
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const std::string& outputFilename) {
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std::ifstream input;
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std::ofstream output;
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if (!openFiles(input, output, inputFilename, outputFilename)) {
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return;
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}
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output << ">marker" << std::endl;
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std::regex pattern("class=BL|^\\s{70}");
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std::string line;
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while (std::getline(input, line)) {
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if (std::regex_search(line, pattern)) {
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std::string processed_line = std::regex_replace(
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line,
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std::regex("</span>|<span class=BL>|^\\s{17}"), "");
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std::replace(processed_line.begin(),
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processed_line.end(), ' ', '-');
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std::replace(processed_line.begin(),
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processed_line.end(), '#', 'm');
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output << processed_line << std::endl;
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}
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}
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closeFiles(input, output);
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}
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int main(int argc, char* argv[]) {
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if (!checkArguments(argc, argv)) {
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return 1;
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}
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processFile(argv[1], argv[2]);
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return 0;
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}
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