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*/
package prop;
import fork.lib.base.file.management.Dirs;
import fork.lib.bio.anno.genomic.BedAttribute;
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 PropLen {
public static void main(String[] args) throws Exception {
File dir= Dirs.getFile("dir");
//File f= new File(dir+"/anno/sgdGene_sacCer1.bed"); String org= "sacCer1";
File f= new File(dir+"/anno/xu_2009_orfs.bed"); String org= "sacCer1-xu";
GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
Iterator<GenomicRegion> it = gb.iterator();
while(it.hasNext()){
GenomicRegion gr= it.next();
Integer len= (int) gr.getRange()+1;
gr.setValue(len);
}
new BedExporter(gb).writeToFile(new File(dir+"/anno/bed/"+org+"/prop/"+org+"_length.bed"));
}
}