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polish: use D instead cpp version

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This commit is contained in:
kuoi 2024-09-10 02:02:03 +10:00
parent 130640eade
commit bc4526da33
2 changed files with 165 additions and 181 deletions
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181
delstop.cpp
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@ -1,181 +0,0 @@
/*
* 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;
}

165
delstop.d Normal file
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import std.file;
import std.stdio;
import std.string;
import std.algorithm;
import std.array;
import std.conv;
// contains taxa and pos
struct TaxaInfo {
string name;
int[] positions;
}
// include TaxaInfo and foundSpecialChar
struct FastaData {
TaxaInfo[] taxaList; // every taxa correspeonds to TaxaInfo
bool foundSpecialChar;
}
void backup(string filePath) {
string backupPath = filePath ~ ".bak";
copy(filePath, backupPath);
}
string replaceSpecialChars(string sequence, const(int)[] positions) {
char[] mutableSequence = sequence.dup; // change to editable
foreach (pos; positions) {
mutableSequence[pos - 1] = '-'; // replace `!` and `*` with `-`
}
sequence = mutableSequence.idup; // change to not editable
return sequence;
}
int[] findSpecialPositions(const string sequence) {
int[] positions;
foreach (i, char c; sequence) {
if (c == '*' || c == '!') {
positions ~= cast(int) (i + 1); // record `int` pos
}
}
return positions;
}
FastaData processFastaAA(string filePath) {
FastaData fastaData; // create struct
string[] lines = File(filePath).byLine().map!(line=>line.to!string).array; // read file
string currentTaxa;
string currentSequence;
string tmpContent;
for (int i = 0; i < lines.length; i++) {
if (lines[i].startsWith(">")) {
if (!currentTaxa.empty) {
// keep last sequence
TaxaInfo taxaInfo;
taxaInfo.name = currentTaxa;
taxaInfo.positions = findSpecialPositions(currentSequence);
fastaData.taxaList ~= taxaInfo; // add TaxaInfo to taxaList
if (taxaInfo.positions.length > 0) {
fastaData.foundSpecialChar = true; // check any special char
}
currentSequence = replaceSpecialChars(currentSequence, taxaInfo.positions); // replace
tmpContent ~= ">" ~ currentTaxa ~ "\n" ~ currentSequence ~ "\n";
currentSequence = ""; // clean prepare next
}
currentTaxa = lines[i][1..$]; // get taxa
} else {
currentSequence ~= lines[i]; // get seq
}
}
// the final one
if (!currentTaxa.empty) {
TaxaInfo taxaInfo;
taxaInfo.name = currentTaxa;
taxaInfo.positions = findSpecialPositions(currentSequence);
fastaData.taxaList ~= taxaInfo;
if (taxaInfo.positions.length > 0) {
fastaData.foundSpecialChar = true;
}
currentSequence = replaceSpecialChars(currentSequence, taxaInfo.positions);
}
if(fastaData.foundSpecialChar){
backup(filePath);
// write back
std.file.write(filePath, tmpContent);
}
return fastaData;
}
void processFastaNT(string filePath, const FastaData fastaData) {
string[] lines = File(filePath).byLine().map!(line=>line.to!string).array; // get fasta_nt
for (int i = 0; i < lines.length; i++) {
if (lines[i].startsWith(">")) {
string currentTaxa = lines[i][1..$];
auto taxaIndex = fastaData.taxaList.countUntil!(t => t.name == currentTaxa); // use countUntil find taxaName
if (taxaIndex != fastaData.taxaList.length) { // if find taxa
int[] positions = fastaData.taxaList[taxaIndex].positions.dup;
int lineIndex = i + 1;
string sequence;
while (lineIndex < lines.length && !lines[lineIndex].startsWith(">")) {
sequence ~= lines[lineIndex]; // get full
lineIndex++;
}
// replace
char[] mutableSequence = sequence.dup;
foreach (pos; positions) {
int startPos = 3 * pos - 2; // 3n-2
int endPos = 3 * pos; // 3n
if (startPos - 1 < mutableSequence.length) {
for (int j = startPos - 1; j < endPos && j < mutableSequence.length; j++) {
mutableSequence[j] = '-'; // 3n-2 to 3n '-'
}
}
}
sequence = mutableSequence.idup;
// write to fasta_nt
int sequencePos = 0;
lineIndex = i + 1;
while (lineIndex < lines.length && !lines[lineIndex].startsWith(">")) {
int len = cast(int) lines[lineIndex].length; // convert to int
lines[lineIndex] = sequence[sequencePos..sequencePos + len];
sequencePos += len;
lineIndex++;
}
}
}
}
// write back
std.file.write(filePath, lines.join("\n"));
}
void processFasta(string fasta_aa, string fasta_nt){
// get pos from fasta_aa & modify
FastaData fastaData = processFastaAA(fasta_aa);
if (fastaData.foundSpecialChar) {
// if found special, proces fasta_nt
// backup fasta_aa
backup(fasta_nt); // modify fasta_nt
processFastaNT(fasta_nt, fastaData); // modify fasta_nt
}
}
void main(string[] args) {
if (args.length < 3) {
writeln("Usage: program <fasta_aa> <fasta_nt>");
return;
}
string fasta_aa = args[1];
string fasta_nt = args[2];
processFasta(fasta_aa, fasta_nt);
}