Examples of writeToFile()

Examples of data.cerevisiae.inhouse.jointable.JoinTable.writeToFile()

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    jj.addBedFile(new File(d+"/swr1-chip_htz1d/swr1-chip_htz1d_sacCer1-xu_gene_three_150.0.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_five_150.0.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_htz1d/swr1-chip_htz1d_sacCer1-xu_gene_five_150.0.bed"));
   
   
    jj.writeToFile(new File(d+"/combine.txt"));
   
   
}
   
   
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Examples of data.cerevisiae.inhouse.jointable.JoinTable.writeToFile()

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    jj.addBedFile(new File(d+"/by4741-wt_ypg_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/by4741-wt_ypg_20140313-r2_pe1_read.bed"));



    jj.writeToFile(new File(d+"/combine.txt"));
   
   
}
   
   
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Examples of data.cerevisiae.region.zpeak.trsc_asso_new.AssoTranscriptionThree.writeToFile()

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    AssoTranscriptionThree ass= new AssoTranscriptionThree(gb, lbf, lbr);
   
    File out= new File(zd+"/asso-trsc_"+zf.getName());
    ass.writeToFile(out);
}

   
   
}
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Examples of data.cerevisiae.test.lineup.LineupSide.writeToFile()

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        File f= fs.get(i);
        if(FileName.getExt(f).equals("wig")){
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            LineupSide ls= new LineupSide(gb, lb);
            File of= new File(od+"/"+FileName.getBaseName(f)+".txt");
            ls.writeToFile(of);
        }
    }


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Examples of data.human.inhouse.chippeak.ScoreMergeChipNorm.writeToFile()

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        System.out.println(f);
        if(FileName.getExt(f).equals("wig")){
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            File out= new File(od+"/chip_"+FileName.getBaseName(f)+".bed");
            ScoreMergeChipNorm ss= new ScoreMergeChipNorm(gb, lb);
            ss.writeToFile(out);
        }
    }
   
}
   
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Examples of data.human.inhouse.chippeak.ScoreMergeChipNorm.writeToFile()

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        System.out.println(f);
        if(FileName.getExt(f).equals("wig")){
            LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
            File out= new File(od+"/chip_"+FileName.getBaseName(f)+".bed");
            ScoreMergeChipNorm ss= new ScoreMergeChipNorm(gb, lb);
            ss.writeToFile(out);
        }
    }
   
}
   
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Examples of data.human.test.trsc.CombineRNA.writeToFile()

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                ifinit=true;
            }
            jj.addBedFile(f);
        }
   
    jj.writeToFile(out);
   
    }


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Examples of data.human.test.trsc.CombineRNA.writeToFile()

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        File ff= new File(rd+"/side-right_200_5_locate_ensGene_hg19_exon_mcf7_rna3_time-"+tms[i]+"_hg19.bed");
        jj.addBedFile(ff);
    }
    */
   
    jj.writeToFile(out);
   
}

   
   
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Examples of data.human.test.trsc.ScoreMergeAgainstRNA.writeToFile()

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        LandscapeBuilder lbf= new BedGraphReader(new File(rnad+"/norm_"+tag+"_for.wig")).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(new File(rnad+"/norm_"+tag+"_rev.wig")).getLandscapeBuilder();
        File outf= new File(od+"/"+FileName.getBaseName(f)+"_"+tag+".bed");
       
        ScoreMergeAgainstRNA ss= new ScoreMergeAgainstRNA(gb, lbf, lbr);
        ss.writeToFile(outf);
    }
   
   
   
}
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Examples of data.human.test.trsc.ScoreMergeAgainstRNA.writeToFile()

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        File od= new File(d+"/scoreRNAEach");
        File outf= new File(od+"/score_"+tag+"_for.bed");
        File outr= new File(od+"/score_"+tag+"_rev.bed");
       
        ScoreMergeAgainstRNA ss= new ScoreMergeAgainstRNA(gb, lbf, lbr);
        ss.writeToFile(outf);
       
        ss= new ScoreMergeAgainstRNA(gb, lbr, lbf);
        ss.writeToFile(outr);
       
    }
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