From 130640eadef0bc40e9640c332f64d5f292de76b4 Mon Sep 17 00:00:00 2001
From: Guoyi Zhang <kuoi@bioarchlinux.org>
Date: Mon, 9 Sep 2024 16:17:15 +1000
Subject: [PATCH] add: C++ software to delete the stop codon

---
 delstop.cpp | 181 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 181 insertions(+)
 create mode 100644 delstop.cpp

diff --git a/delstop.cpp b/delstop.cpp
new file mode 100644
index 0000000..911b1ac
--- /dev/null
+++ b/delstop.cpp
@@ -0,0 +1,181 @@
+/*
+ * This script is for deleting stop codon
+ * in both AA and original_NT files
+ * Copyright
+ * Guoyi Zhang, UNSW & Australian Museum
+ */
+
+#include <filesystem>
+#include <fstream>
+#include <iostream>
+#include <string>
+#include <unordered_map>
+#include <vector>
+
+namespace fs = std::filesystem;
+
+class FastaProcessor {
+      public:
+	FastaProcessor(const std::string& inputFile,
+		       const std::string& outputFile)
+	    : input_file(inputFile), output_file(outputFile) {}
+
+	void processFile() {
+		// bakup input file
+		std::string backup_file = input_file + ".bak";
+		fs::copy_file(input_file, backup_file,
+			      fs::copy_options::overwrite_existing);
+
+		std::ifstream infile(input_file);
+		std::ofstream outfile(input_file + ".tmp");  // temp file
+		std::string line;
+
+		while (std::getline(infile, line)) {
+			if (line[0] == '>') {
+				if (!sequence.empty()) {
+					positions_map[taxa] =
+					    processSequence(sequence);
+					outfile << taxa << "\n"
+						<< sequence << "\n";
+				}
+				taxa = line;
+				sequence.clear();
+			} else {
+				sequence = line;
+			}
+		}
+
+		// process final taxa
+		if (!sequence.empty()) {
+			positions_map[taxa] = processSequence(sequence);
+			outfile << taxa << "\n" << sequence << "\n";
+		}
+
+		infile.close();
+		outfile.close();
+
+		// overwrite with temp file
+		fs::rename(input_file + ".tmp", input_file);
+
+		// process same name file
+		if (fs::exists(output_file)) {
+			// backup outputfile
+			std::string output_backup_file = output_file + ".bak";
+			fs::copy_file(output_file, output_backup_file,
+				      fs::copy_options::overwrite_existing);
+
+			processOutputFile();
+			fs::rename(output_file + ".tmp", output_file);
+		}
+	}
+
+      private:
+	std::string input_file;
+	std::string output_file;
+	std::string taxa;
+	std::string sequence;
+	std::unordered_map<std::string, std::vector<size_t>> positions_map;
+
+	std::vector<size_t> processSequence(std::string& sequence) {
+		std::vector<size_t> positions;
+		size_t non_dash_index = 0;
+
+		for (size_t i = 0; i < sequence.size(); ++i) {
+			if (sequence[i] != '-') {
+				non_dash_index++;
+				if (sequence[i] == '!' || sequence[i] == '*') {
+					positions.push_back(
+					    non_dash_index);  // pos without -
+					sequence[i] = '-';    // replace with -
+				}
+			}
+		}
+		return positions;
+	}
+
+	void processOutputFile() {
+		std::ifstream infile(output_file);
+		std::ofstream outfile(output_file + ".tmp");
+		std::string line;
+		std::string current_taxa;
+		std::string current_sequence;
+
+		while (std::getline(infile, line)) {
+			if (line[0] == '>') {
+				if (!current_sequence.empty() &&
+				    positions_map.find(current_taxa) !=
+					positions_map.end()) {
+					replacePositions(
+					    current_sequence,
+					    positions_map[current_taxa]);
+					outfile << current_taxa << "\n"
+						<< current_sequence << "\n";
+				}
+				current_taxa = line;
+				current_sequence.clear();
+			} else {
+				current_sequence = line;
+			}
+		}
+
+		// process final taxa
+		if (!current_sequence.empty() &&
+		    positions_map.find(current_taxa) != positions_map.end()) {
+			replacePositions(current_sequence,
+					 positions_map[current_taxa]);
+			outfile << current_taxa << "\n"
+				<< current_sequence << "\n";
+		}
+
+		infile.close();
+		outfile.close();
+	}
+
+	void replacePositions(std::string& sequence,
+			      const std::vector<size_t>& positions) {
+		std::string new_sequence = sequence;
+		size_t sequence_length = sequence.size();
+
+		for (size_t pos : positions) {
+			size_t start = (pos * 3) - 3;  //  3n-2
+			size_t end = pos * 3;	       //  3n
+
+			if (start < sequence_length) {
+				for (size_t i = start;
+				     i < end && i < sequence_length; ++i) {
+					new_sequence[i] = '-';
+				}
+			}
+		}
+
+		sequence = new_sequence;
+	}
+};
+
+int main(int argc, char* argv[]) {
+	if (argc != 3) {
+		std::cerr << "Usage: " << argv[0]
+			  << " <input_folder> <output_folder>" << std::endl;
+		return 1;
+	}
+
+	std::string input_folder = argv[1];
+	std::string output_folder = argv[2];
+
+	// get all fasta
+	for (const auto& entry : fs::directory_iterator(input_folder)) {
+		if (entry.path().extension() == ".fasta" ||
+		    entry.path().extension() == ".fas") {
+			std::string input_file = entry.path().string();
+			std::string output_file =
+			    output_folder + "/" +
+			    entry.path().filename().string();
+
+			FastaProcessor processor(input_file, output_file);
+			processor.processFile();
+		}
+	}
+
+	return 0;
+}
+