Examples of addBedFile()

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

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    Arrays.sort(fs);
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(f.isDirectory() && ! f.getName().equals("plot")){
            String fn= FileName.getBaseName(f);
            jj.addBedFile(new File(d+"/"+fn+"/"+fn+"_sacCer1-xu_gene_five_0.150.bed"));
            jj.addBedFile(new File(d+"/"+fn+"/"+fn+"_sacCer1-xu_gene_three_150.0.bed"));
        }
    }
   
    jj.writeToFile(new File(d+"/combine.txt"));
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Examples of data.cerevisiae.inhouse.jointable.JoinTable.addBedFile()

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    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(f.isDirectory() && ! f.getName().equals("plot")){
            String fn= FileName.getBaseName(f);
            jj.addBedFile(new File(d+"/"+fn+"/"+fn+"_sacCer1-xu_gene_five_0.150.bed"));
            jj.addBedFile(new File(d+"/"+fn+"/"+fn+"_sacCer1-xu_gene_three_150.0.bed"));
        }
    }
   
    jj.writeToFile(new File(d+"/combine.txt"));
   
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Examples of data.cerevisiae.inhouse.jointable.JoinTable.addBedFile()

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    JoinTable jj= new JoinTable();
    jj.initRows(ref);
   
   
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_five_0.150.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_three_150.0.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_htz1d/swr1-chip_htz1d_sacCer1-xu_gene_five_0.150.bed"));
    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"));
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Examples of data.cerevisiae.inhouse.jointable.JoinTable.addBedFile()

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    JoinTable jj= new JoinTable();
    jj.initRows(ref);
   
   
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_five_0.150.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_three_150.0.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_htz1d/swr1-chip_htz1d_sacCer1-xu_gene_five_0.150.bed"));
    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"));
   
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Examples of data.cerevisiae.inhouse.jointable.JoinTable.addBedFile()

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    jj.initRows(ref);
   
   
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_five_0.150.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_three_150.0.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_htz1d/swr1-chip_htz1d_sacCer1-xu_gene_five_0.150.bed"));
    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"));
   
   
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Examples of data.cerevisiae.inhouse.jointable.JoinTable.addBedFile()

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    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_five_0.150.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_three_150.0.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_htz1d/swr1-chip_htz1d_sacCer1-xu_gene_five_0.150.bed"));
    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.addBedFile()

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    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_five_0.150.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_three_150.0.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_htz1d/swr1-chip_htz1d_sacCer1-xu_gene_five_0.150.bed"));
    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.addBedFile()

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    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_five_0.150.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_wt/swr1-chip_wt_sacCer1-xu_gene_three_150.0.bed"));
    jj.addBedFile(new File(d+"/swr1-chip_htz1d/swr1-chip_htz1d_sacCer1-xu_gene_five_0.150.bed"));
    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.addBedFile()

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    ReadTable rt= new ReadTable(new File(refd+"/anno_ercc-rna_spike-in.txt"));
    rt.param().setSkipRows(0);
    jj.addHashMapIDToVal(rt.getHashMap(1, 3), "conc");
   
   
    jj.addBedFile(new File(d+"/569-4kr-cen_sd-ura_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/569-4kr-cen_sd-ura_20140313-r2_pe1_read.bed"));
    jj.addBedFile(new File(d+"/666-htz1-cen_sd-ura_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/666-htz1-cen_sd-ura_20140313-r2_pe1_read.bed"));
    jj.addBedFile(new File(d+"/749-htz1oe_ypg_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/749-htz1oe_ypg_20140313-r2_pe1_read.bed"));
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Examples of data.cerevisiae.inhouse.jointable.JoinTable.addBedFile()

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    rt.param().setSkipRows(0);
    jj.addHashMapIDToVal(rt.getHashMap(1, 3), "conc");
   
   
    jj.addBedFile(new File(d+"/569-4kr-cen_sd-ura_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/569-4kr-cen_sd-ura_20140313-r2_pe1_read.bed"));
    jj.addBedFile(new File(d+"/666-htz1-cen_sd-ura_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/666-htz1-cen_sd-ura_20140313-r2_pe1_read.bed"));
    jj.addBedFile(new File(d+"/749-htz1oe_ypg_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/749-htz1oe_ypg_20140313-r2_pe1_read.bed"));
    jj.addBedFile(new File(d+"/1054-wt-gdna_sd-ura_20140313-r1_pe1_read.bed"));
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