commit c601a8b65f1832439e64e37d3137fe0cf5ed10b3
Author: Guoyi Zhang <kuoi@bioarchlinux.org>
Date:   Tue May 7 12:33:05 2024 +0800

    init

diff --git a/gene_marker.cpp b/gene_marker.cpp
new file mode 100644
index 0000000..ee03857
--- /dev/null
+++ b/gene_marker.cpp
@@ -0,0 +1,88 @@
+/*
+ * Author: Guoyi Zhang
+ * Date: 07 May 2024
+ * License: GPLv2
+ * Function: Generate fasta file which `m`
+ * 	means selected position by Gblocks
+ * 	from Gblocks html report file.
+ * */
+
+#include <fstream>
+#include <iostream>
+#include <regex>
+#include <string>
+
+bool checkArguments(int argc, char* argv[]) {
+	if (argc != 3) {
+		std::cerr << "Usage: " << argv[0]
+			  << " input_file output_file\n";
+		return false;
+	}
+	return true;
+}
+
+bool openFiles(std::ifstream& input, std::ofstream& output,
+	       const std::string& inputFilename,
+	       const std::string& outputFilename) {
+	input.open(inputFilename);
+	if (!input.is_open()) {
+		std::cerr << "Unable to open input file: " << inputFilename
+			  << std::endl;
+		return false;
+	}
+
+	output.open(outputFilename);
+	if (!output.is_open()) {
+		std::cerr << "Unable to open output file: " << outputFilename
+			  << std::endl;
+		input.close();
+		return false;
+	}
+
+	return true;
+}
+
+void closeFiles(std::ifstream& input, std::ofstream& output) {
+	input.close();
+	output.close();
+}
+
+void processFile(const std::string& inputFilename,
+		 const std::string& outputFilename) {
+	std::ifstream input;
+	std::ofstream output;
+
+	if (!openFiles(input, output, inputFilename, outputFilename)) {
+		return;
+	}
+
+	output << ">marker" << std::endl;
+
+	std::regex pattern("class=BL|^\\s{70}");
+	std::string line;
+	while (std::getline(input, line)) {
+		if (std::regex_search(line, pattern)) {
+			std::string processed_line = std::regex_replace(
+			    line,
+			    std::regex("</span>|<span class=BL>|^\\s{17}"), "");
+			std::replace(processed_line.begin(),
+				     processed_line.end(), ' ', '-');
+			std::replace(processed_line.begin(),
+				     processed_line.end(), '#', 'm');
+			output << processed_line << std::endl;
+		}
+	}
+
+	closeFiles(input, output);
+}
+
+int main(int argc, char* argv[]) {
+	if (!checkArguments(argc, argv)) {
+		return 1;
+	}
+
+	processFile(argv[1], argv[2]);
+
+	return 0;
+}
+
diff --git a/trim_marker.cpp b/trim_marker.cpp
new file mode 100644
index 0000000..8c04ce1
--- /dev/null
+++ b/trim_marker.cpp
@@ -0,0 +1,115 @@
+/*
+ * Author: Guoyi Zhang
+ * Date: 07 May 2024
+ * License: GPLv2
+ * Function: Trim the multi-sequence-
+ * 	alignment based on the marker
+ * 	which `m` indicates selected
+ * 	position.
+ * */
+
+#include <fstream>
+#include <iostream>
+#include <string>
+#include <vector>
+
+// Function: check the arg
+void check_argument_count(int argc, char* argv[]) {
+	if (argc != 4) {
+		std::cerr
+		    << "Usage: " << argv[0]
+		    << " <marker_fasta_file> <input_fasta_file> <output_file>"
+		    << std::endl;
+		exit(1);
+	}
+}
+
+// Function: check the file
+void check_file_exists(const std::string& file) {
+	std::ifstream infile(file);
+	if (!infile.good()) {
+		std::cerr << "Error: file " << file << " doesn't exsit"
+			  << std::endl;
+		exit(1);
+	}
+}
+
+// Function: get the positions in marker file
+std::vector<int> read_positions(const std::string& file) {
+	std::ifstream infile(file);
+	std::string line;
+	std::vector<int> positions;
+	int index = 1;
+	while (std::getline(infile, line)) {
+		if (line[0] != '>') {
+			for (char c : line) {
+				if (c == 'm' || c == 'M') {
+					positions.push_back(index);
+				}
+				index++;
+			}
+		}
+	}
+	return positions;
+}
+
+// Function: trimming the sequences in input_fasta_file
+void extract_characters(const std::string& line, const std::string& file,
+			const std::vector<int> positions) {
+	std::ofstream outfile(file, std::ios::app);
+	std::string new_line;
+	for (int pos : positions) {
+		if (pos <= line.length()) {
+			new_line += line[pos - 1];  // start from 0
+		}
+	}
+	for (size_t i = 0; i < new_line.length(); i += 60) {
+		int num_chars =
+		    std::min(static_cast<int>(new_line.length() - i), 60);
+		outfile << new_line.substr(i, num_chars) << std::endl;
+	}
+	outfile.close();
+}
+
+// Function: parse the fasta multi-lines format
+void process_fasta_file(const std::string& fasta_file,
+			const std::string& output_file,
+			const std::vector<int> positions) {
+	std::ifstream infile(fasta_file);
+	std::string line;
+	std::string prev_line = "";
+	bool prev_line_is_header = false;
+	while (std::getline(infile, line)) {
+		if (line[0] == '>') {
+			if (!prev_line_is_header) {
+				extract_characters(prev_line, output_file,
+						   positions);
+			}
+			std::ofstream outfile(output_file, std::ios::app);
+			outfile << line << std::endl;
+			outfile.close();
+			prev_line_is_header = true;
+		} else {
+			if (prev_line_is_header) {
+				prev_line = "";
+				prev_line_is_header = false;
+			}
+			prev_line += line;
+		}
+	}
+	extract_characters(prev_line, output_file, positions);
+}
+
+int main(int argc, char* argv[]) {
+	check_argument_count(argc, argv);
+
+	for (int i = 1; i <= 2; i++) {
+		check_file_exists(argv[i]);
+	}
+
+	std::vector<int> positions = read_positions(argv[1]);
+
+	process_fasta_file(argv[2], argv[3], positions);
+
+	return 0;
+}