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package data.cerevisiae.test;
import fork.lib.base.file.management.Dirs;
import fork.lib.bio.anno.genomic.BedReader;
import fork.lib.bio.anno.genomic.BedReaderParam;
import fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder;
import fork.lib.bio.anno.genomic.region.GenomicRegionsModifier;
import java.io.File;
import data.cerevisiae.region.GenerateGenic;
/**
*
* @author muxin gu
*/
public class Generate {
protected GenomicRegionsBuilder gb;
public Generate(GenomicRegionsBuilder gb){
this.gb=gb;
init();
}
protected void init(){}
public void writeToDirectory(File od, String org) throws Exception{
GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
gm.getFivePrimeEnds(200, 200).writeToFileBed(new File(od+"/"+org+"_gene_five_200.200.bed"));
gm.getGenicRegions(200, 200).writeToFileBed(new File(od+"/"+org+"_gene_cds_200.200.bed"));
gm.getThreePrimeEnds(200, 200).writeToFileBed(new File(od+"/"+org+"_gene_three_200.200.bed"));
new GenomicRegionsModifier(gm.getAllIntergenicRegions()).getGenicRegions(200, 200) .writeToFileBed(new File(od+"/"+org+"_intergenic_200.bed"));
}
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";
File od= new File(dir+"/anno/bed/"+org+"/200");
BedReaderParam par= new BedReaderParam();
par.ifDirectional=true;
GenomicRegionsBuilder gb= new BedReader(f, par).getGenomicRegionsBuilder();
Generate gg= new Generate(gb);
gg.writeToDirectory(od, org);
}
}