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package data.human.inhouse.cuff;
import fork.lib.base.file.management.Dirs;
import fork.lib.bio.anno.genomic.BedExporter;
import fork.lib.bio.anno.genomic.region.GenomicRegion;
import fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
/**
*
* @author man-mqbpjmg4
*/
public class ExtractNovel {
public static void main(String[] args) throws Exception { //debug
File dir= Dirs.getFile("dir");
File d= new File(dir+"/data/human_magnus/rna/cuff/time-5");
File f= new File(d+"/genes.fpkm_tracking");
File of= new File(d+"/novel_"+f.getName()+".bed");
GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
BufferedReader br= new BufferedReader(new FileReader(f));
String l;
while((l=br.readLine())!=null){
String[] ss= l.split("\t");
String id= ss[0];
String loc= ss[6];
if(id.contains("CUFF")){
GenomicRegion gr= GenomicRegion.parseGenomicRegoinUCSC(loc);
gr.setID(id);
gbout.add(gr);
}
}
br.close();
new BedExporter(gbout).writeToFile(of);
}
}