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package data.cerevisiae.region.aclen;
import fork.lib.base.file.io.txt.ReadTable;
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.region.GenomicRegion;
import fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder;
import fork.lib.bio.anno.genomic.region.GenomicRegionsLocator;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.text.DecimalFormat;
import java.util.Iterator;
/**
*
* @author forksapien
*/
public class Locate {
static double[] zs= new double[]{
0, 20, 40
};
static double[] acs= new double[]{
0, 2, 10, 20, 40,1000
};
public static void main(String[] args) throws Exception {
File dir= Dirs.getFile("dir");
File d= new File(dir+"/anno/bed/len/score");
File od= new File(d+"/select_ac");
od.mkdirs();
File rf= new File(dir+"/anno/xu_2009_orfs.bed");
for( int i=0; i<zs.length ; i++ ){
double z= zs[i];
for( int j=0; j<acs.length ; j++ ){
double ac= acs[j];
File fa= new File(d+"/score_norm_htz1_len_150.bed");
File fb= new File(d+"/score_norm_k8ac_len_150.bed");
GenomicRegionsBuilder gba= new BedReader(fa).getGenomicRegionsBuilder();
GenomicRegionsBuilder gbb= new BedReader(fb).getGenomicRegionsBuilder();
GenomicRegionsBuilder gbde= new GenomicRegionsBuilder();
GenomicRegionsBuilder gbac= new GenomicRegionsBuilder();
Iterator<GenomicRegion> ita= gba.iterator();
Iterator<GenomicRegion> itb= gbb.iterator();
while(ita.hasNext()){
GenomicRegion ra= ita.next();
GenomicRegion rb= itb.next();
double va= ra.getValue();
double vb= rb.getValue();
if(va>z){
rb.setID(Double.toString(va)+"_"+Double.toString(vb));
rb.setValue(0);
if(vb<ac){
gbde.add(rb);
}else{
gbac.add(rb);
}
}
}
String tag= "z"+z+"_ac"+ac;
new BedExporter(gbde).writeToFile(new File(od+"/select-de_"+tag+".bed"));
GenomicRegionsLocator gl= new GenomicRegionsLocator(
gbde,
new BedReader(rf).getGenomicRegionsBuilder()
);
gl.writeToSeparateFiles(
new File(od+"/locate-de_"+tag+"_in.txt"),
new File(od+"/locate-de_"+tag+"_between.txt")
);
new BedExporter(gbac).writeToFile(new File(od+"/select-ac_"+tag+".bed"));
gl= new GenomicRegionsLocator(
gbac,
new BedReader(rf).getGenomicRegionsBuilder()
);
gl.writeToSeparateFiles(
new File(od+"/locate-ac_"+tag+"_in.txt"),
new File(od+"/locate-ac_"+tag+"_between.txt")
);
}
}
}
}