Question

如何用python将fastq转化为fasta

Answer 1

/*
* fq2fa.cpp
* convert fastq to fasta
*

#include <iostream>
#include <fstream>
#include <cstring>
#include <cstdlib>
using namespace std;

long line = 0;
int main(int argc,char *argv[])
{
ifstream fin;
ofstream fout;
if(argc != 3) {
cout << "ERROR: illegal argument number: " << argc << endl;
cout << "Uasage: \n \t fq2fa fastaq_file fasta_file \n" <<endl;
exit(0);
}

fin.open(argv[1]);
fout.open(argv[2]);
if(!fin.good()) {
cout << "ERROR: illegal input file path: " << argv[1] <<endl;
cout << "Uasage: \n \t fq2fa fastaq_file fasta_file \n" <<endl;
exit(0);
}
else if(!fout.good()) {
cout << "ERROR: illegal output file path" << endl;
cout << "Uasage: \n \t fq2fa fastaq_file fasta_file \n" <<endl;
exit(0);
}
cout << "Converting Data..." << endl;
int mod;
line=0;
while(fin != NULL) {
string s;
getline(fin,s,'\n');
if (s==""){
continue;
}
line=line+1;
mod=line % 4;
if (mod == 1){
s[0]='>';
fout << s << endl;
}
if (mod == 2){
fout << s << endl;
}
}
cout << "finished!" << endl;
fout.close();
fin.close();
return 0;
}

g++ -o fq2fa fq2fa.cpp 编译即可