Package data.cerevisiae.inhouse.jointable

Examples of data.cerevisiae.inhouse.jointable.JoinTable

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    File dir= Dirs.getFile("dir");
    File d= new File(dir+"/other_datasets/harbison_2004");
   
    File f= new File(d+"/pvalbygene_forpaper_abbr.txt");
   
    JoinTable jj= new JoinTable();
    jj.initRows( new File(dir+"/anno/xu_2009_orfs.bed") );
   
   
    jj.addTextFileChunk(f);
   
    jj.writeToFile(new File(d+"/combine.txt"));
   
   
}
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public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
    File ref= new File(dir+"/anno/xu_2009_orfs.bed");
    File d= new File(dir+"/other_datasets\\liu_2005_hist-mods\\data\\wig\\score");
   
    JoinTable jj= new JoinTable();
    jj.initRows(ref);
   
    File[] fs= d.listFiles();
    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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    File dir= Dirs.getFile("dir");
    File nf= new File(dir+"/anno/sgd_name.bed");
    File ref= new File(dir+"/anno/xu_2009_orfs.bed");
   
   
    JoinTable jj= new JoinTable();
   
   
    jj.initRows(ref);
    jj.addNameBedFile(nf);
   
    File wd= new File(dir+"/other_datasets\\lenstra_2011\\GSE25909_RAW\\idmap\\norm\\plot/");
    File inf= new File(wd+"/combine_raw.txt");
    ReadTable rt= new ReadTable(inf);
    String[] cols= rt.getTableAsArray()[0];
    for( int i=1; i<cols.length; i++ ){
        jj.addHashMapIDToVal(rt.getHashMap(0, i), cols[i]);
    }

    File out= new File(wd+"/combine.txt");
    jj.writeToFile(out);
   
}
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public static void main(String[] args) throws Exception { //debug
    File dir= Dirs.getFile("dir");
    File ref= new File(dir+"/anno/xu_2009_orfs.bed");
    File d= new File(dir+"/other_datasets\\ranjan2013_swr1-chip\\score");
   
    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"));
   
   
    jj.writeToFile(new File(d+"/combine.txt"));
   
   
}
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    File d= new File(dir+"/data\\spikein\\score");
    File refd= new File(dir+"/anno/genomes/spikein/ercc_rna");
    File ref= new File(refd+"/ercc-rna_spike-in.bed");
   
   
    JoinTable jj= new JoinTable();
   
    jj.initRows(ref);
   
   
    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"));
    jj.addBedFile(new File(d+"/1054-wt-gdna_sd-ura_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/1054-wt-gdna_sd-ura_20140313-r2_pe1_read.bed"));
    jj.addBedFile(new File(d+"/1057-htz1-2um_sd-ura_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/1057-htz1-2um_sd-ura_20140313-r2_pe1_read.bed"));
    jj.addBedFile(new File(d+"/1058-4kr-2um_sd-ura_20140313-r1_pe1_read.bed"));
    jj.addBedFile(new File(d+"/1058-4kr-2um_sd-ura_20140313-r2_pe1_read.bed"));
    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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    File dir= Dirs.getFile("dir");
    File nf= new File(dir+"/anno/sgd_name.bed");
    File ref= new File(dir+"/anno/xu_2009_orfs.bed");
    File d= new File(dir+"/data/chip-seq\\norm\\score\\sacCer1-xu\\219-swr1d_r1");
   
    JoinTable jj= new JoinTable();
   
   
    jj.initRows(ref);
    jj.addNameBedFile(nf);
   
    File wd= new File(dir+"/other_datasets/inhouse/swr1d");
    wd.mkdirs();
   
    jj.addBedFile(new File(d+"/219-swr1d_r1_sacCer1-xu_gene_five_0.150.bed"));
    jj.addBedFile(new File(d+"/219-swr1d_r1_sacCer1-xu_gene_three_150.0.bed"));
   

    File out= new File(wd+"/combine.txt");
    jj.writeToFile(out);
   
}
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Related Classes of data.cerevisiae.inhouse.jointable.JoinTable

  • data.cerevisiae.harbison.JoinTableHar
  • data.cerevisiae.histmod.liu2005_histmods.JoinTableL
  • data.cerevisiae.inhouse.inhouseswr1.JoinTables
  • data.cerevisiae.inhouse.spikein.JoinTableERCC
  • data.cerevisiae.lenstra2011.JoinTables
  • data.cerevisiae.ranjan2013swr1.JoinTable1
  • fork.lib.base.file.io.txt.ReadTable
  • java.io.File
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