将fastq转为fasta的代码

/*
 * fq2fa.cpp 
* convert fastq to fasta 
*
* Copyright@Wang Jiawei, BGI Shenzhen, China, 2012-11-29 
* The Latest revision@Wang Jiawei, BGI Shenzhen, China, 2012-11-29 
*/

#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