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import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.util.Scanner;
import java.util.regex.*;

/**
 *
 */

/**
 * @author Administrator
 *
 */
public class Test {

 /**
  *
  */
 public Test() {
  // TODO Auto-generated constructor stub
 }

 /**
  * @param args
  * @throws IOException
  */
 public static void main(String[] args) throws IOException {
  // TODO Auto-generated method stub

  Scanner stdin = new Scanner(System.in);

  System.out.println("ÇëÊäÈë°üº¬ËùÓлùÒò¼Ò×åblastÎļþµÄÎļþÃû,È磺/path/file:");

  String geneFamily_blast_all = stdin.nextLine();

  // ÊäÈë°üº¬ËùÓÐȾɫÌåÐòÁÐÎļþĿ¼µÄÎļþ,¶à¸öȾɫÌåÐòÁÐ
  Scanner chromoStdin = new Scanner(System.in);

  System.out.println("ÇëÊäÈë°üº¬È¾É«ÌåÐòÁÐÎļþµÄÎļþÃû,È磺/path/file:");

  String chromo_all = chromoStdin.nextLine();

  FileReader geneFamily_blast_freader = null;

  BufferedReader geneFamily_blast_breader = null;

  // FileReader chromo_all_freader = null;
  // BufferedReader chromo_all_breader = null;
  RandomAccessFile rf = null;

  try {
   geneFamily_blast_freader = new FileReader(geneFamily_blast_all);
   geneFamily_blast_breader = new BufferedReader(
     geneFamily_blast_freader);

   // chromo_all_freader = new FileReader(chromo_all);
   // chromo_all_breader = new BufferedReader(chromo_all_freader);

   rf = new RandomAccessFile(chromo_all, "rw");
  } catch (FileNotFoundException e) {
   // TODO Auto-generated catch block
   e.printStackTrace();
   System.out.println("geneFamily_blast_all File Not Found!");
  }
  String geneFamily_blast_filepath = "";
  String chromo_all_filepath = "";
  /*
   * ÊäÈë·¾¶ÊÇÕâÖÖÇé¿ö£ºD:\statistic\rice_genomices\chromosome01.fasta ģʽÓÃÏÂÃæµÄ
   * Pattern pattern = Pattern.compile("[\\\\.]"); Èç¹û
   * ·¾¶ÊÇÕâÑùµÄ£¬D:/statistic/rice_genomices/chromosome01.fasta ÔòÓÃPattern
   * pattern = Pattern.compile("[/\\.]");
   */
  Pattern pattern = Pattern.compile("[/\\.]");
  String[] strs1 = null;
  String[] strs2 = null;
  String genefamily_out = "";
  while ((geneFamily_blast_filepath = geneFamily_blast_breader.readLine()) != null) {

   strs1 = pattern.split(geneFamily_blast_filepath);

     int i=0;
   
           
   while ((chromo_all_filepath = rf.readLine()) != null) {
    
    i=i+1;
    strs2 = pattern.split(chromo_all_filepath);
    genefamily_out = strs1[4] + "_" + strs2[3] + "." + strs2[4];

    System.out.println("genefamily_out  " + genefamily_out);

    /*
     * for (int i = 0; i < strs1.length; i++) { System.out.println(i
     * + strs1[i]); }
     */
   }
   if (i==12) {
    rf.seek(0);
   }
  }
 }

 /*
  * for (int i = 0; i < strs2.length; i++) { System.out.println(i +
  * strs2[i]); }
  */
}