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sort_by_size.cpp
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sort_by_size.cpp
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#include <fstream>
#include <cstring>
#include <string>
#include <vector>
#include <iostream>
#include <algorithm>
#include <cstdint>
using namespace std;
string getLineFasta(ifstream* in){
string line,result;
getline(*in,line);
char c=in->peek();
while(c!='>' and c!=EOF){
getline(*in,line);
result+=line;
c=in->peek();
}
return result;
}
void clean(string& str){
for(unsigned int i(0); i< str.size(); ++i){
switch(str[i]){
case 'a':break;
case 'A':break;
case 'c':break;
case 'C':break;
case 'g':break;
case 'G':break;
case 't':break;
case 'T':break;
default: str="";return;
}
}
transform(str.begin(), str.end(), str.begin(), ::toupper);
}
bool myfunction (pair<string,string> i,pair<string,string> j) { return (i.second.size()>j.second.size()); }
int main(int argc, char ** argv){
vector<pair<string,string>> reads;
if(argc<2){
cout<<"[Fasta file] "<<endl;
exit(0);
}
string input(argv[1]);
bool cleaning(false);
if(argc>2){
cleaning=true;
}
srand (time(NULL));
string header, sequence,line;
ifstream in(input);
vector<unsigned int> lengths;
while(not in.eof()){
getline(in,header);
if(header[0]!='>'){continue;}
char c=in.peek();
while(c!='>' and c!=EOF){
getline(in,line);
sequence+=line;
c=in.peek();
}
//~ cout<<header<<'\n'<<sequence<<"\n";
reads.push_back({(header),sequence});
sequence="";
}
sort(reads.begin(),reads.end(),myfunction);
for(unsigned int i(0);i<reads.size();++i){
cout<<">"<<reads[i].first<<"\n"<<reads[i].second<<"\n";
}
}