polish: use D instead cpp version
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130640eade
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2 changed files with 165 additions and 181 deletions
181
delstop.cpp
181
delstop.cpp
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@ -1,181 +0,0 @@
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/*
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* This script is for deleting stop codon
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* in both AA and original_NT files
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* Copyright
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* Guoyi Zhang, UNSW & Australian Museum
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*/
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#include <filesystem>
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#include <fstream>
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#include <iostream>
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#include <string>
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#include <unordered_map>
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#include <vector>
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namespace fs = std::filesystem;
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class FastaProcessor {
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public:
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FastaProcessor(const std::string& inputFile,
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const std::string& outputFile)
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: input_file(inputFile), output_file(outputFile) {}
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void processFile() {
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// bakup input file
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std::string backup_file = input_file + ".bak";
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fs::copy_file(input_file, backup_file,
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fs::copy_options::overwrite_existing);
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std::ifstream infile(input_file);
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std::ofstream outfile(input_file + ".tmp"); // temp file
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std::string line;
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while (std::getline(infile, line)) {
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if (line[0] == '>') {
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if (!sequence.empty()) {
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positions_map[taxa] =
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processSequence(sequence);
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outfile << taxa << "\n"
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<< sequence << "\n";
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}
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taxa = line;
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sequence.clear();
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} else {
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sequence = line;
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}
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}
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// process final taxa
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if (!sequence.empty()) {
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positions_map[taxa] = processSequence(sequence);
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outfile << taxa << "\n" << sequence << "\n";
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}
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infile.close();
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outfile.close();
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// overwrite with temp file
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fs::rename(input_file + ".tmp", input_file);
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// process same name file
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if (fs::exists(output_file)) {
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// backup outputfile
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std::string output_backup_file = output_file + ".bak";
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fs::copy_file(output_file, output_backup_file,
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fs::copy_options::overwrite_existing);
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processOutputFile();
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fs::rename(output_file + ".tmp", output_file);
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}
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}
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private:
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std::string input_file;
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std::string output_file;
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std::string taxa;
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std::string sequence;
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std::unordered_map<std::string, std::vector<size_t>> positions_map;
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std::vector<size_t> processSequence(std::string& sequence) {
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std::vector<size_t> positions;
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size_t non_dash_index = 0;
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for (size_t i = 0; i < sequence.size(); ++i) {
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if (sequence[i] != '-') {
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non_dash_index++;
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if (sequence[i] == '!' || sequence[i] == '*') {
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positions.push_back(
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non_dash_index); // pos without -
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sequence[i] = '-'; // replace with -
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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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void processOutputFile() {
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std::ifstream infile(output_file);
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std::ofstream outfile(output_file + ".tmp");
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std::string line;
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std::string current_taxa;
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std::string current_sequence;
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while (std::getline(infile, line)) {
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if (line[0] == '>') {
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if (!current_sequence.empty() &&
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positions_map.find(current_taxa) !=
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positions_map.end()) {
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replacePositions(
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current_sequence,
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positions_map[current_taxa]);
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outfile << current_taxa << "\n"
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<< current_sequence << "\n";
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}
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current_taxa = line;
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current_sequence.clear();
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} else {
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current_sequence = line;
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}
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}
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// process final taxa
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if (!current_sequence.empty() &&
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positions_map.find(current_taxa) != positions_map.end()) {
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replacePositions(current_sequence,
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positions_map[current_taxa]);
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outfile << current_taxa << "\n"
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<< current_sequence << "\n";
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}
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infile.close();
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outfile.close();
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}
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void replacePositions(std::string& sequence,
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const std::vector<size_t>& positions) {
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std::string new_sequence = sequence;
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size_t sequence_length = sequence.size();
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for (size_t pos : positions) {
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size_t start = (pos * 3) - 3; // 3n-2
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size_t end = pos * 3; // 3n
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if (start < sequence_length) {
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for (size_t i = start;
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i < end && i < sequence_length; ++i) {
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new_sequence[i] = '-';
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}
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}
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}
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sequence = new_sequence;
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}
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};
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int main(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_folder> <output_folder>" << std::endl;
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return 1;
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}
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std::string input_folder = argv[1];
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std::string output_folder = argv[2];
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// get all fasta
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for (const auto& entry : fs::directory_iterator(input_folder)) {
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if (entry.path().extension() == ".fasta" ||
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entry.path().extension() == ".fas") {
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std::string input_file = entry.path().string();
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std::string output_file =
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output_folder + "/" +
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entry.path().filename().string();
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FastaProcessor processor(input_file, output_file);
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processor.processFile();
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}
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}
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return 0;
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}
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165
delstop.d
Normal file
165
delstop.d
Normal file
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@ -0,0 +1,165 @@
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import std.file;
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import std.stdio;
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import std.string;
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import std.algorithm;
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import std.array;
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import std.conv;
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// contains taxa and pos
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struct TaxaInfo {
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string name;
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int[] positions;
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}
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// include TaxaInfo and foundSpecialChar
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struct FastaData {
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TaxaInfo[] taxaList; // every taxa correspeonds to TaxaInfo
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bool foundSpecialChar;
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}
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void backup(string filePath) {
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string backupPath = filePath ~ ".bak";
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copy(filePath, backupPath);
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}
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string replaceSpecialChars(string sequence, const(int)[] positions) {
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char[] mutableSequence = sequence.dup; // change to editable
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foreach (pos; positions) {
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mutableSequence[pos - 1] = '-'; // replace `!` and `*` with `-`
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}
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sequence = mutableSequence.idup; // change to not editable
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return sequence;
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}
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int[] findSpecialPositions(const string sequence) {
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int[] positions;
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foreach (i, char c; sequence) {
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if (c == '*' || c == '!') {
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positions ~= cast(int) (i + 1); // record `int` pos
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}
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}
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return positions;
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}
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FastaData processFastaAA(string filePath) {
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FastaData fastaData; // create struct
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string[] lines = File(filePath).byLine().map!(line=>line.to!string).array; // read file
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string currentTaxa;
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string currentSequence;
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string tmpContent;
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for (int i = 0; i < lines.length; i++) {
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if (lines[i].startsWith(">")) {
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if (!currentTaxa.empty) {
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// keep last sequence
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TaxaInfo taxaInfo;
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taxaInfo.name = currentTaxa;
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taxaInfo.positions = findSpecialPositions(currentSequence);
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fastaData.taxaList ~= taxaInfo; // add TaxaInfo to taxaList
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if (taxaInfo.positions.length > 0) {
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fastaData.foundSpecialChar = true; // check any special char
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}
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currentSequence = replaceSpecialChars(currentSequence, taxaInfo.positions); // replace
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tmpContent ~= ">" ~ currentTaxa ~ "\n" ~ currentSequence ~ "\n";
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currentSequence = ""; // clean prepare next
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}
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currentTaxa = lines[i][1..$]; // get taxa
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} else {
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currentSequence ~= lines[i]; // get seq
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}
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}
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// the final one
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if (!currentTaxa.empty) {
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TaxaInfo taxaInfo;
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taxaInfo.name = currentTaxa;
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taxaInfo.positions = findSpecialPositions(currentSequence);
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fastaData.taxaList ~= taxaInfo;
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if (taxaInfo.positions.length > 0) {
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fastaData.foundSpecialChar = true;
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}
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currentSequence = replaceSpecialChars(currentSequence, taxaInfo.positions);
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}
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if(fastaData.foundSpecialChar){
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backup(filePath);
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// write back
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std.file.write(filePath, tmpContent);
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}
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return fastaData;
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}
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void processFastaNT(string filePath, const FastaData fastaData) {
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string[] lines = File(filePath).byLine().map!(line=>line.to!string).array; // get fasta_nt
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for (int i = 0; i < lines.length; i++) {
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if (lines[i].startsWith(">")) {
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string currentTaxa = lines[i][1..$];
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auto taxaIndex = fastaData.taxaList.countUntil!(t => t.name == currentTaxa); // use countUntil find taxaName
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if (taxaIndex != fastaData.taxaList.length) { // if find taxa
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int[] positions = fastaData.taxaList[taxaIndex].positions.dup;
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int lineIndex = i + 1;
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string sequence;
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while (lineIndex < lines.length && !lines[lineIndex].startsWith(">")) {
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sequence ~= lines[lineIndex]; // get full
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lineIndex++;
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}
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// replace
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char[] mutableSequence = sequence.dup;
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foreach (pos; positions) {
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int startPos = 3 * pos - 2; // 3n-2
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int endPos = 3 * pos; // 3n
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if (startPos - 1 < mutableSequence.length) {
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for (int j = startPos - 1; j < endPos && j < mutableSequence.length; j++) {
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mutableSequence[j] = '-'; // 3n-2 to 3n '-'
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}
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}
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}
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sequence = mutableSequence.idup;
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// write to fasta_nt
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int sequencePos = 0;
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lineIndex = i + 1;
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while (lineIndex < lines.length && !lines[lineIndex].startsWith(">")) {
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int len = cast(int) lines[lineIndex].length; // convert to int
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lines[lineIndex] = sequence[sequencePos..sequencePos + len];
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sequencePos += len;
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lineIndex++;
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}
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}
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}
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}
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// write back
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std.file.write(filePath, lines.join("\n"));
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}
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void processFasta(string fasta_aa, string fasta_nt){
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// get pos from fasta_aa & modify
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FastaData fastaData = processFastaAA(fasta_aa);
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if (fastaData.foundSpecialChar) {
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// if found special, proces fasta_nt
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// backup fasta_aa
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backup(fasta_nt); // modify fasta_nt
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processFastaNT(fasta_nt, fastaData); // modify fasta_nt
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}
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}
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void main(string[] args) {
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if (args.length < 3) {
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writeln("Usage: program <fasta_aa> <fasta_nt>");
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return;
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}
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string fasta_aa = args[1];
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string fasta_nt = args[2];
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processFasta(fasta_aa, fasta_nt);
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}
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