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package data.human.statham2014mods;
import fork.lib.base.file.FileName;
import fork.lib.base.file.management.Dirs;
import fork.lib.bio.anno.genomic.BedReader;
import fork.lib.bio.anno.genomic.SplicedBedReader;
import fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder;
import fork.lib.bio.anno.genomic.region.SplicedRegionsLocator;
import java.io.File;
/**
*
* @author man-mqbpjmg4
*/
public class Locate {
public static void main(String[] args) throws Exception { //debug
File dir= Dirs.getFile("dir");
File d= new File(dir+"/other_datasets/statham2014_mcf7-mods/norm/peaks");
File anno= new File(dir+"/anno/ensGene_hg19_exon.bed");
File[] fs = d.listFiles();
for( int i=0; i<fs.length; i++ ){
File f= fs[i];
if(FileName.getExt(f).equals("bed")){
GenomicRegionsBuilder peaks= new BedReader(f).getGenomicRegionsBuilder();
SplicedBedReader sr= new SplicedBedReader(anno);
File od= new File(d+"/locate/"+ FileName.getBaseName(anno));
File odt= new File(od+"/"+FileName.getBaseName(f));
SplicedRegionsLocator ll= new SplicedRegionsLocator(peaks, sr);
ll.writeToDir(odt, "locate");
ll.writeToFile(new File(od+"/locate_"+f.getName()));
}
}
}
}