FastQ数据质量值转换

  • A+
所属分类:Script

不同的平台测出来的数据采用的质量编码格式一般会有差异。关于FastQ的格式介绍可以阅读《FastQ格式介绍》

譬如sanger的编码采用的是质量值+33,而Soleax采用的是质量值+64。有时候由于特殊情况需要转换一下编码格式,用perl写有点麻烦而且运行速度也不咋地。下面给大家推荐一款我自己用c++写的程序。

在该程序的第58行,readqual[i]=readqual[i] +31; 由于我们这个程序是把phred33编码格式转换成Soleax64的,新的编码格式里面每个字母的质量需要增加31. 如果用于其他转码用途大家自己根据需要改一下这一行就可以了。

 

#include <iostream>
#include <fstream>
#include <cstring>
#include <cstdlib>

using namespace std;
int main(int argc,char *argv[])
{
ifstream Readsin; // 输入文件句柄
ofstream Readsout; // 输出文件句柄

if(argc != 3)//三个参数,这个值是3,还有一个是程序名称
{
cout << "ERROR: illegal argument number: " << argc << endl;
cout << "Usage:\n"
<< "\tInput format:\n"
<< "\t\tphred33to64 FastaqFile_33 FastaqFile_64 \n" << endl;
exit(0);
}

Readsin.open(argv[1]);//参数从1开始,0是名称
Readsout.open(argv[2]);

if(!Readsin.good()) // 检查 输入文件是否存在以及被打开
{
cout << "ERROR: illegal input file path: " << argv[1] <<endl;
cout << "Usage:\n"
<< "\tInput format:\n"
<< "\t\tphred33to64 FastaqFile_33 FastaqFile_64 \n" << endl;
exit(0);
}
if(!Readsin.good()) // 检查 输出文件是否可以被创建
{
cout << "ERROR: illegal input file path: " << argv[2] <<endl;
cout << "Usage:\n"
<< "\tInput format:\n"
<< "\t\tphred33to64 FastaqFile_33 FastaqFile_64 \n" << endl;
exit(0);
}
//
cout << "Filtering Reads ...." << endl;
string readname;
string readseq;
string readlinker;
string readqual;
int Readslength;
while (Readsin != NULL)
{
getline(Readsin,readname,'\n');
getline(Readsin,readseq,'\n');
getline(Readsin,readlinker,'\n');
getline(Readsin,readqual,'\n');

Readslength=readseq.length();

for (int i=0;i<Readslength;i++)
{
readqual[i]=readqual[i] +31;//修改31来自定义该软件的转码方式
}
Readsout << readname << endl;
Readsout << readseq << endl;
Readsout << readlinker<<endl;
Readsout << readqual << endl;
}
Readsout.close();
Readsin.close();
return 0;
}

 

avatar

发表评论

:?: :razz: :sad: :evil: :!: :smile: :oops: :grin: :eek: :shock: :???: :cool: :lol: :mad: :twisted: :roll: :wink: :idea: :arrow: :neutral: :cry: :mrgreen: