/*
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*/
package data.cerevisiae.test;
import fork.lib.base.file.io.txt.ReadTable;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
/**
*
* @author muxin gu
*/
public class Class {
public static void main(String[] args) throws Exception { //debug
File d= new File("G:\\mystudy\\phd\\files\\anno\\bed\\sacCer1-xu\\200\\out");
String[][] arr= new ReadTable(new File(d+"/score_sacCer1-xu_gene_cds_200.200.bed")).getTableAsArray();
String[] v5s= new ReadTable(new File(d+"/score_sacCer1-xu_gene_five_200.200.bed")).getColumn(4);
String[] v3s= new ReadTable(new File(d+"/score_sacCer1-xu_gene_three_200.200.bed")).getColumn(4);
String[] vcds= new ReadTable(new File(d+"/score_sacCer1-xu_gene_cds_200.200.bed")).getColumn(4);
String[] vis= new ReadTable(new File(d+"/score_sacCer1-xu_intergenic_200.bed")).getColumn(4);
File out= new File(d+"/clas.bed");
BufferedWriter bw= new BufferedWriter(new FileWriter(out));
for( int i=0; i<arr.length; i++ ){
String[] r= arr[i];
String v5= v5s[i], v3=v3s[i], vcd=vcds[i], vi=vis[i];
String s;
if(!vi.equals("0")){
s="intergenic";
}else if(!vcd.equals("0")){
if(!v5.equals("0")){
s="5";
}else{
s="cds";
}
}else if(!v5.equals("0")){
s="5";
}else if(!v3.equals("0")){
s="3";
}else{
//System.out.println("xxx");
s="intergenic";
}
bw.write(r[0]+"\t"+r[1]+"\t"+r[2]+"\t"+r[3]+"\t"+s+"\t"+r[5]+"\n");
}
}
}