Package fork.lib.bio.anno.genomic

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

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    LandscapeTransformer lt= new LandscapeTransformer(lb);
    lt.selectLength(300, Integer.MAX_VALUE);
    double sum= lb.totalArea();
    double fac= sum/Math.pow(10, 8);
    lt.divideBy( fac );
    new BedGraphExporter(lb).writeToFile(outNorm);
}
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public void writeToDir(File od)throws Exception {
    double sum = lbf.totalArea()+ lbr.totalArea();
    double fac= sum/ Math.pow(10, 10);
    LandscapeTransformer ltf= new LandscapeTransformer(lbf);
    ltf.divideBy(fac);
    new BedGraphExporter(lbf).writeToFile(new File(od+"/norm_"+tag+"_for.wig"));
    LandscapeTransformer ltr= new LandscapeTransformer(lbr);
    ltr.divideBy(fac);
    new BedGraphExporter(lbr).writeToFile(new File(od+"/norm_"+tag+"_rev.wig"));
}
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            }
        }
    }
   
   
    BedGraphExporter be =new BedGraphExporter(lb);
    be.param().tit= FileName.getBaseName(out);
    be.writeToFile(out);
}
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    LandscapeTransformer lt= new LandscapeTransformer(lb);
    lt.unlog(2);
   
    File of= new File(d+"/unlog2_"+ f.getName());
    new BedGraphExporter(lb).writeToFile(of);
}
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        File f= fs[i];
        if(FileName.getExt(f).equals("bar")){
            LandscapeBuilder lb= new BarReader(f).getLandscapeBuilder();

            File of= new File(d+"/"+FileName.getBaseName(f)+".wig");
            new BedGraphExporter(lb).writeToFile(of);;
        }
    }
}
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            LandscapeTransformer lt= new LandscapeTransformer(lb);
            lt.unlog();
           
            File of= new File(d+"/unlog_"+FileName.getBaseName(f)+".wig");
            new BedGraphExporter(lb).writeToFile(of);;
        }
    }
}
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                lb.add(chr, reg);
            }
            pp=p; pv=v;
        }
       
        BedGraphExporter be= new BedGraphExporter(lb);
        be.appendToFile(bw);
    }
    bw.close();
}
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    System.out.println("subfac: "+fac);
   
    Distribution dnz= lb.getDistributionNonZero();
    double nf= dnz.sum()/ 100000000;
    new LandscapeTransformer(lb).divideBy(nf);
    BedGraphExporter be= new BedGraphExporter(lb);
    be.param().tit= tit;
    be.writeToFile(f);
}
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            //System.out.println(fval+"    "+ ival+"   "+ fr.getRange());
            nv= nv<0 ? 0 : nv;
            fr.setAttribute(nv);
            lbout.add(chr, fr);
        }
        BedGraphExporter be= new BedGraphExporter(lbout);
        be.appendToFile(bw);
    }
    bw.close();
    System.out.println();
   
}
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    LandscapeTransformer lt= new LandscapeTransformer(lb);
    lt.selectLength(150, Integer.MAX_VALUE);
    double sum= lb.totalArea();
    double fac= sum/Math.pow(10, 8);
    lt.divideBy( fac );
    new BedGraphExporter(lb).writeToFile(out);
}
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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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