還是沒能忍住，想看一下用JAVA語言處理上一篇文章的任務能快多少，畢竟編譯語言遠快於腳本語言。廢話不多說，直接上代碼：

import java.io.FileReader;
import java.io.BufferedReader;
import java.io.BufferedWriter;  
import java.io.FileWriter;
import java.io.IOException;

public class Split{
    public static void main(String[] args) throws IOException
    {
        
 
long startTime = System.currentTimeMillis();
        BufferedReader read_line = new BufferedReader(new FileReader("head_10000000.vcf"), 5000000);
        BufferedWriter write_line = new BufferedWriter(new FileWriter("result.tsv"), 5000000);
        String current_line = read_line.readLine();
        while(current_line != null
 
)
        {
            while(current_line.startsWith("#"))
            {
                current_line = read_line.readLine();
            }
            String[] split1 = current_line.split("\t");
            String info = split1[7];
            String[] split2 = info.split(";AF=");
            String str1 
 
= split2[1];
            String[] split3 = str1.split(";");
            write_line.write(current_line + "    " + split3[0]);
            write_line.newLine();
            current_line = read_line.readLine();
        }
        write_line.flush();
        write_line.close();
        read_line.close();
        long endTime = System.currentTimeMillis();
        System.out.println("run time:"+(endTime-startTime)+"ms");
    }
}

　程序運行結果：

run time:47473ms

　檢驗結果：

$ wc -l result.tsv 
10000000 result.tsv

$ sed -n ‘3435534p‘ result.tsv 
2    29509274    rs114511873    C    A    100    PASS    AA=C;AN=2184;AVGPOST=0.9997;VT=SNP;THETA=0.0006;AC=14;SNPSOURCE=LOWCOV;LDAF=0.0065;ERATE=0.0003;RSQ=0.9798;AF=0.01;AFR_AF=0.03    0.01

$ sed -n ‘7546563p‘ result.tsv 
3    84580386    rs191768644    T    C    100    PASS    RSQ=0.6088;AA=T;AN=2184;VT=SNP;AVGPOST=0.9991;SNPSOURCE=LOWCOV;AC=1;THETA=0.0007;ERATE=0.0002;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020    0.0005

$ sed -n ‘987345p‘ result.tsv 
1    74709013    rs185004386    A    C    100    PASS    AN=2184;LDAF=0.0018;THETA=0.0005;VT=SNP;AA=A;SNPSOURCE=LOWCOV;RSQ=0.7110;ERATE=0.0003;AVGPOST=0.9987;AC=3;AF=0.0014;ASN_AF=0.01    0.0014 

　　我們檢查了文件的總行數以及隨機抽取了若幹行，發現結果正確。相比較於前面的R語言計算效率，這個結果表示十分震驚！ 相差太遠！！！

Time（java代碼編寫 + 編譯 + 運行） < Time(R腳本運行)

利用JAVA完成上述的操作