/*
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*/
package prop.clas;
import fork.lib.bio.anno.genomic.BedExporter;
import fork.lib.bio.anno.genomic.BedReader;
import fork.lib.bio.anno.genomic.BedReaderParam;
import fork.lib.bio.anno.genomic.region.GenomicRegion;
import fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder;
import fork.lib.math.algebra.elementary.set.continuous.Region;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.util.ArrayList;
import java.util.Iterator;
/**
*
* @author forksapien
*/
public class ClassChr {
public static void main(String[] args) throws Exception {
File dir= new File("/home/forksapien/mystudy/phd/files");
//File dir= new File("G:/mystudy/phd/files");
File f= new File(dir+"/anno/sgdGene_sacCer1.bed");
GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
File out = new File(dir+"/anno/clas/clas_chr.txt");
out.getParentFile().mkdirs();
BufferedWriter bw= new BufferedWriter(new FileWriter(out));
String[] chrs= gb.getChromosomeList();
for( int i=0; i<chrs.length ; i++ ){
String chr= chrs[i];
bw.write(">"+chr+"\n");
ArrayList<Region> al = gb.getRegionsForChromosome(chr);
for( int j=0; j<al.size() ; j++ ){
String n= ((GenomicRegion)al.get(j)).attr.toString();
bw.write(n+"\n");
}
}
bw.close();
}
}