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package data.cerevisiae.region.scan;
import fork.lib.base.file.FileName;
import fork.lib.base.file.management.Dirs;
import fork.lib.bio.anno.genomic.BedExporter;
import fork.lib.bio.anno.genomic.BedGraphBuffer;
import fork.lib.bio.anno.genomic.BedReader;
import fork.lib.bio.anno.genomic.LandscapeBuffer;
import fork.lib.bio.anno.genomic.LandscapeScoringResultEntry;
import fork.lib.bio.anno.genomic.LandscapeScoringStrand;
import fork.lib.bio.anno.genomic.region.DirectionalGenomicRegion;
import fork.lib.bio.anno.genomic.region.GenomicRegion;
import fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder;
import fork.lib.bio.anno.genomic.region.GenomicRegionsModifier;
import fork.lib.math.algebra.advanced.linearalgebra.Vector;
import fork.lib.math.algebra.elementary.set.continuous.Region;
import fork.lib.math.algebra.elementary.set.continuous.RegionException;
import fork.lib.math.applied.buffer.Landscape2DBuffer;
import java.io.File;
import java.util.ArrayList;
import java.util.Iterator;
/**
*
* @author forksapien
*/
public class LinkAntisense {
protected GenomicRegionsBuilder gb;
protected LandscapeBuffer lbf, lbr;
protected ArrayList<LandscapeScoringResultEntry> ress;
/** bp ousdie genes */
public int out= 50;
/** bp from the mid point */
public int side= 20;
public LinkAntisense(GenomicRegionsBuilder gb, LandscapeBuffer lbf, LandscapeBuffer lbr) throws Exception{
this.gb=gb;
this.lbf=lbf;
this.lbr=lbr;
init();
}
protected void init() throws Exception{
ress= new ArrayList<>();
GenomicRegionsBuilder ggg= new GenomicRegionsModifier(new GenomicRegionsModifier(gb).getComplementaryStrand()).getExtendedRegions(out, out);
LandscapeScoringStrand ls= new LandscapeScoringStrand(lbf, lbr, ggg
){
protected double[] scoreStrand(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
return Landscape2DBuffer.getLandscape(bufs, gr);
}
};
ArrayList<LandscapeScoringResultEntry> rs= ls.getResultEntries();
for( int i=0; i<rs.size() ; i++ ){
DirectionalGenomicRegion gr= (DirectionalGenomicRegion)rs.get(i).gr;
double[] vs= rs.get(i).scores;
int mid= vs.length/2;
int fl, fh, tl, th;
if(gr.isOnForwardStrand()){
fl=0;
fh= mid- side;
tl= mid+ side;
th= vs.length-1;
}else{
tl= 0;
th= mid- side;
fl= mid+side;
fh= vs.length-1;
}
//System.out.println();gr.printInt();System.out.println(vs.length);System.out.println(fl+" "+fh);
Vector vec= new Vector(vs);
double vf= vec.subset(fl, fh).toDistribution().mean();
double vt= vec.subset(tl, th).toDistribution().mean();
double[] ft= new double[]{vf, vt};
ress.add(new LandscapeScoringResultEntry(gr,ft));
}
}
public void writeToFile(File out) throws Exception{
GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
for( int i=0; i<ress.size() ; i++ ){
LandscapeScoringResultEntry r=ress.get(i);
GenomicRegion ge= r.gr;
Object o= ge.attr==null ? ge.toUCSCFormat() : ge.attr;
ge.attr= new Object[]{o,
new Double(r.scores[0]), new Double(r.scores[1])
};
gbout.add(ge);
}
gbout.sortAll();
BedExporter be= new BedExporter(gbout){
protected String column3(GenomicRegion gr){
return ((Object[])gr.attr)[0].toString();
}
protected String column4(GenomicRegion gr){
return gr.toUCSCFormat();
}
protected String column6On(GenomicRegion gr){
Object[] os= (Object[])gr.attr;
return (Double)os[1]+"\t"+ (Double)os[2];
}
};
be.param().ifExpanded= true;
be.writeToFile(out);
}
public static void main(String[] args) throws Exception {
File dir= Dirs.getFile("dir");
File fd= new File(dir+"/data/rna");
File f= new File("out/score/set/sacCer1-xu/scan/intra_300_0_10_51.bed");
GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
String s= "884-rrp6d-wt";
LandscapeBuffer lbf= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_for.wig"));
LandscapeBuffer lbr= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_rev.wig"));
System.out.println(1);
LinkAntisense ll= new LinkAntisense(gb, lbf, lbr);
//LinkAntisense ll= new LinkAntisense(gb, null, null);
ll.writeToFile(new File("out/score/set/sacCer1-xu/scan/linkAnti_"+FileName.getBaseName(f) +".bed"));
}
}