112 lines
4.4 KiB
C++
112 lines
4.4 KiB
C++
#include <array>
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#include <chrono>
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#include <cstddef>
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#include <cstdio>
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#include <exception>
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#include <filesystem>
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#include<fstream>
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#include <sstream>
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#include <stdexcept>
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#include<algorithm>
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#include"tools.hpp" // 自己写的库，在src/tools/tools.hpp当中，注意要使用C++23标准编译
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#include <cstring>
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#include <string_view>
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#include <type_traits>
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#include <unordered_map>
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// 这两个宏用来申请读入和读出流，实现反射并输出日志，获取申请流的变量名字
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#define OPEN_IFS_AND_CHECK(file_path,value_name)std::ifstream value_name(file_path);if(value_name.is_open()==false){std::stringstream ss;ss<<"cannot open input file stream : "<<file_path.filename();throw std::runtime_error(ss.str());}else{zt::print("Open input file stream to value ["#value_name"] ok , from [",file_path.filename(),"]\n");}
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#define OPEN_OFS_AND_CHECK(file_path,value_name)std::ofstream value_name(file_path);if(value_name.is_open()==false){std::stringstream ss;ss<<"cannot open output file stream : "<<file_path.filename();throw std::runtime_error(ss.str());}else{zt::print("Open output file stream to value ["#value_name"] ok , from [",file_path.filename(),"]\n");}
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//最大DNA序列长度
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const size_t MAX_SIZE = 5e4+5;
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void reverseComplement(std::array<char, MAX_SIZE> &DNAsequence, const size_t buf_size) //注意这里使用引用DNA sequence，避免拷贝开销
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{
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static const std::unordered_map<char, char> complement = { //这里使用查表的方式大大提高CPU速度，因为if分支CPU不容易命中缓存，需要使用查表加速
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{'A', 'T'}, {'a', 'T'},
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{'T', 'A'}, {'t', 'A'},
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{'C', 'G'}, {'c', 'G'},
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{'G', 'C'}, {'g', 'C'}
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};
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std::reverse(DNAsequence.begin(), DNAsequence.begin() + buf_size); //翻转DNA序列
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for (std::remove_const_t<decltype(buf_size)> i = 0; i < buf_size; ++i) {
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auto it = complement.find(DNAsequence[i]);//查表并替换
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if (it != complement.end()) {
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DNAsequence[i] = it->second;
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}
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}
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}
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class Spent{ // 使用RAII原理的自动计时器，计算主函数运行时间，析构时自动输出
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private:
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const decltype(std::chrono::system_clock::now()) start;
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const std::string_view name;
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public:
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Spent(std::string_view name)noexcept:start(std::chrono::system_clock::now()),name(name){
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zt::print("[Timer: ",name,"]"," Start timing","\n");
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}
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~Spent()noexcept{
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const auto end = std::chrono::system_clock::now();
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const auto dur = std::chrono::duration_cast<std::chrono::milliseconds> (end-start);
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zt::print("[Timer: ",name,"]"," Stop timing , using ", dur,"\n");
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}
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};
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int main()
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{
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try{
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std::ios_base::sync_with_stdio(false); //加了没效果
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using namespace std;
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Spent all_spent("All spent"); //自动计时器，给主函数计时
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std::array<char,MAX_SIZE> buf;
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unsigned long long lines = 0;
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filesystem::path input_path("filteredReads.txt"),output_path("reversedSequence.txt");
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// ifstream input_file_stream(input_path);
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// ofstream output_file_stream(output_path);
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OPEN_IFS_AND_CHECK(input_path, input_file_stream) //创建输入和输出流
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OPEN_OFS_AND_CHECK(output_path, output_file_stream)
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// string l = "";
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zt::print("Undergoing transformation\n");
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while (input_file_stream.getline(buf.data(),MAX_SIZE,'\n'))
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{
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int m = lines%2;
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const auto buf_len = strlen(buf.data());
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const std::string_view suffix("\n"); //设置一个每个DNA序列结尾的字符，这里是以\n换行来结尾
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if (m == 1){
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// output_file_stream << reverseComplement(buf) << endl;
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reverseComplement(buf,buf_len);
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}
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for(int i=0;i<suffix.size();i++){
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buf[buf_len+i]=suffix[i]; // 将末尾增加字符追加到结尾。注意不能过长超过MAX_SIZE
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}
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output_file_stream.write(buf.data(), buf_len+suffix.size()); // 写入文件
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lines++;
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}
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return 0;
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}catch(const std::exception &e){
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zt::print(
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"Caught an error because:\n",
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"\t",NAME_VALUE(e.what()),"\n"
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"Closing\n"
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);
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}catch(...){
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zt::print(
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"Caught an unknown error because:\n",
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"Closing\n"
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);
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}
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return -1;
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}
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