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oneLineBreak.cpp
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oneLineBreak.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, unsigned int sizeMin){
string out;
for(unsigned int i(0); i< str.size(); ++i){
switch(str[i]){
case 'a':out+="A";break;
case 'A':out+="A";break;
case 'c':out+="C";break;
case 'C':out+="C";break;
case 'g':out+="G";break;
case 'G':out+="G";break;
case 't':out+="T";break;
case 'T':out+="T";break;
default: if (out.size()> sizeMin){cout<<">x\n"<<out<<"\n";}out="";break;
}
}
if (out.size()> sizeMin){cout<<">x\n"<<out<<"\n";}
}
int main(int argc, char ** argv){
if(argc<2){
cout<<"[Fasta file] [minSize]"<<endl;
exit(0);
}
string input(argv[1]);
unsigned int cleaning(stoi(argv[2]));
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();
}
clean(sequence,cleaning);
sequence="";
}
}