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extract_reads.cpp
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extract_reads.cpp
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#include <fstream>
#include <string.h>
#include <iostream>
#include <list>
#include "robin_hood.h"
#include <cstdint>
using namespace std;
typedef robin_hood::unordered_flat_map<string,bool> Map;
string split_1(string chaine, char del ){
string re ="";
int size(chaine.size());
int i(0);
while(chaine[i] != del and i<size){
re += chaine[i];
i++;
}
return re;
}
int main(int argc, char** argv){
if(argc<2){
cout<<"[sequence name file] [fasta file]"<<endl;
return 0;
}
string file_names_seq=argv[1];
string file_fasta=argv[2];
Map names_seq;
ifstream flux(file_names_seq.c_str());
string ligne;
if(flux){
ligne.clear();
while(getline(flux, ligne)){
if(ligne.size()>0){
names_seq[ligne]=true;
// cout<<"insert"<<ligne<<"end"<<endl;
}
}
}else{
cout << "ERROR: Unable to open the file." << endl;
exit(0);
}
flux.close();
flux.open(file_fasta.c_str());
string name_seq_fasta;
if(flux){
ligne.clear();
bool found(false);
while(getline(flux, ligne)){
if(ligne.size()>0){
if (ligne[0] == '>'){
found=false;
name_seq_fasta=split_1(ligne.substr(1, ligne.size()-1),' ');
if (names_seq[name_seq_fasta]) {
found=true;
// cout<<"FOUND"<<endl;
cout << ligne << '\n';
}else{
// cout<<"NOP"<<ligne<<"END"<<endl;
}
}
else{
if (found) {
cout << ligne << '\n';
}
}
}
}
}
else{
cout << "ERROR: Unable to open the file." << endl;
exit(0);
}
flux.close();
return 0;
}