Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.BedGraphExporter

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    write(ids, vs, orev, "reverse", tag);
}

protected void write(ArrayList<String> ids, ArrayList<Double> vs, File f,String std, String tag)throws Exception{
    ProbeMapperStrand pp= new ProbeMapperStrand(anno, probe, std);
    BedGraphExporter be= new BedGraphExporter(pp.toLandscapeBuilder(ids, vs));
    be.param().tit= tag+"_"+std;
    be.writeToFile(f);
}
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            }
        }
    }
   
   
    BedGraphExporter be =new BedGraphExporter(lb);
    be.param().tit= FileName.getBaseName(out);
    be.writeToFile(out);
}
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                }
            }
        }
    }
   
    BedGraphExporter be= new BedGraphExporter(lbout);
    be.param().tit= FileName.getBaseName(out);
    be.writeToFile(out);
}
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public static void toWig(File tas, File out, String tit)throws Exception{
    TASIntensityReader tr= new TASIntensityReader(tas);
    new BedGraphExporter(tr.toLandscapeBuilder(), tit).writeToFile(out);
}
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    for( int i=0; i<chrs.length ; i++ ){
        String chr= chrs[i];
        LandscapeBuilder lbt= new LandscapeBuilder();
        lbt.addAll(chr, lb.getLandscape2DForChromosome(chr));
        new LandscapeTransformer(lbt).unlog(Math.E);
        BedGraphExporter be= new BedGraphExporter(lbt);
        be.appendToFile(bw);
    }
    bw.close();
}
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public static void normalise(LandscapeBuilder lb, File of, String tit, double seqDepth) throws Exception{
    new LandscapeTransformer(lb).selectLength(100, Double.POSITIVE_INFINITY);
    new LandscapeTransformer(lb).divideBy( (seqDepth)/1000000 );
   
    BedGraphExporter be= new BedGraphExporter(lb){
        public void appendToFile(BufferedWriter bw) throws IOException{
            String[] chrs= lb.getChromosomeList();
            for( int j=0; j<chrs.length ; j++ ){
                String chr= chrs[j];
                ArrayList<Region> rs= lb.getLandscape2DForChromosome(chr).getRegions();
                if(rs!=null && rs.size()>=1){
                    for( int i=0; i<rs.size() ; i++ ){
                        Region r = rs.get(i);
                        double v= Double.parseDouble(r.attr.toString());
                        if(v!=0 & r.low>0){
                            bw.write(chr+"\t"+
                                    (int)r.low+"\t"+
                                    (int)(r.high+1)+"\t"+
                                    format(v)+"\n");
                        }
                    }
                }
            }
        }
    };
    be.param().tit= tit;
    be.writeToFile(of);
}
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public void writeToFiles(File f, File r) throws Exception{
    BedGraphExporterParam par = new BedGraphExporterParam();
    par.tit= FileName.getBaseName(f);
    par.df= new DecimalFormat("#.##");
    new BedGraphExporter(lbf, par).writeToFile(f);
   
    par.tit= FileName.getBaseName(r);
    new BedGraphExporter(lbr, par).writeToFile(r);
}
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Related Classes of fork.lib.bio.anno.genomic.BedGraphExporter

  • data.cerevisiae.ConsToWig
  • data.cerevisiae.histmod.cai2011.ToWig
  • data.cerevisiae.histmod.guillemett2011_h3k4.Unlog
  • data.cerevisiae.histmod.guillemette2011.ToWig
  • data.cerevisiae.histmod.kirmizis2009.ProbeMapper
  • data.cerevisiae.histmod.xue2012.BarToWig
  • data.cerevisiae.histmod.xue2012.Unlog
  • data.cerevisiae.inhouse.a_norm.NormChipChip
  • data.cerevisiae.inhouse.a_norm.NormChipChipSignal
  • data.cerevisiae.inhouse.a_norm.NormChipSeqRPM
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