Package fork.lib.base.file.io.txt

Examples of fork.lib.base.file.io.txt.ReadTable

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    }
   
   
   
protected void init() throws Exception{
    ReadTable rt= new ReadTable(f);
    String[][] arr= rt.getTableAsArray();
    String[] cns= arr[0];
    for(int i=1; i<cns.length ; i++){
        String n= cns[i];
        n= n.replace("_YPD", "");
        n= n.replace("(", "");
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    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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    sets.add(new GeneSet(tag+"_h5h3"));
    sets.add(new GeneSet(tag+"_l5l3"));
    sets.add(new GeneSet(tag+"_l5h3"));
    sets.add(new GeneSet(tag+"_n"));

    String[] ids= new ReadTable(fu).getColumn(3);
    double[] v5s= FormatOp1D.objToDouble( new ReadTable(fu).getColumn(4) );
    double[] v3s= FormatOp1D.objToDouble( new ReadTable(fd).getColumn(4) );
    for(int i=0; i<v5s.length ; i++){
        String id= ids[i];
        double v5= v5s[i];
        double v3= v3s[i];
        if(v5>50){
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public void writeToFile(File out) throws Exception{
    out.getParentFile().mkdirs();
    String[][] arr= new ReadTable(f).getTableAsArray();
    String[] cns= arr[0];
    for(int i=1; i<cns.length ; i++){
        String tf= cns[i];
        tf= tf.replace("_YPD", "");
        tf= tf.replace("(", "");
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private void init() throws Exception{
    gb= new GenomicRegionsBuilder();
    ReadTable rt= new ReadTable(f);
    String[][] arr= rt.getTableAsArray();
    for( int i=0; i<arr.length ; i++ ){
        String [] r= arr[i];
        GenomicRegion gr= UCSCRegionParser.parseGenomicRegion(r[4]).getExtendedRegion(-50, -50);
        double vf= Double.parseDouble(r[6]);
        double vt= Double.parseDouble(r[7]);
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    double fold= 2; double diff= 30;
   
    File fa= new File(d+"/score_norm_"+a+"_len_150.bed");
    File fb= new File(d+"/score_norm_"+b+"_len_150.bed");
   
    ReadTable rt= new ReadTable(fa);
    String[][] a1= rt.getTableAsArray();
    rt= new ReadTable(fb);
    String[][] a2= rt.getTableAsArray();
   
    DecimalFormat df= new DecimalFormat("#.##");
    String tag= a+"_"+b+"_"+fold+"_"+diff;
    BufferedWriter bwup= new BufferedWriter(new FileWriter(new File(sd+"/select_"+tag+"_up.bed")));
    BufferedWriter bwdown= new BufferedWriter(new FileWriter(new File(sd+"/select_"+tag+"_down.bed")));
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    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"));
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            double ac= acs[j];
   
            File f= new File(d+"/locate-"+deac+"_z"+z+"_ac"+ac+"_in.txt"); int tar= 8;
            System.out.println(f.getName());

            ReadTable rt= new ReadTable(f);
            String[] cs= rt.getColumn(tar);

            FrequencyCount<String> ff= new FrequencyCount<>(cs);
            Print.map(ff.getFrequencyCounts());
            System.out.println();
        }
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    File out= new File(d+"/map_"+ f.getName());
    out.getParentFile().mkdirs();
   
    ReadTable rt=  new ReadTable(f);
    BufferedWriter bw= new BufferedWriter(new FileWriter(out));
    String[][] arr= rt.getTableAsArray();
    for( int i=0; i<arr.length ; i++ ){
        String[] r= arr[i];
        for( int j=0; j<=7 ; j++ ){
            bw.write(r[j]+"\t");
        }
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    File d= new File(dir+"/other_datasets/statham2014_mcf7-mods/");
    File f= new File(d+"/GSM1383850_MCF7_NDR.bed");
    File anno= new File(dir+"/anno/ensGene_hg19_exon.bed");
   
    GenomicRegionsBuilder gb= new GenomicRegionsBuilder();
    ReadTable rt= new ReadTable(f);
    Table<String> tab= rt.getTable();
    for( int i=0; i<tab.getRowNumber(); i++ ){
        ArrayList<String> r= tab.getRow(i);
        DirectionalGenomicRegion gr= new DirectionalGenomicRegion(
                r.get(0),
                '+',
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