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

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

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    Arrays.sort(fs);
    for(int i=0; i<fs.length ; i++){
        File df= fs[i];
        String nm= df.getName();
        File f= new File(df+"/"+nm+"_sacCer1-xu_gene_five_300.0.bed");
        ReadTable rt= new ReadTable(f);
        String[] rns= rt.getColumn(3);
        String[] vs= rt.getColumn(4);
        if(i==0){
            for(int j=0; j<rns.length ; j++){
                String rn= rns[j];
                tab.appendEmptyRow(rn);
            }
            ReadTable rtt= new ReadTable(new File(dir+"/anno/sgd_name.bed"));
            HashMap<String,String> hm= rtt.getHashMap(3, 4);
            ArrayList<String> rows= tab.getRowNames();
            tab.appendEmptyColumn("common_name");
            for(int j=0; j<rows.size() ; j++){
                String row= rows.get(j);
                if(hm.containsKey(row)){
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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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    JoinTableS jj= new JoinTableS();
   
   
    jj.initEmptyRow(new ReadTable(fa).getColumn(0));
   
    jj.addTextFile(fa);
    jj.addTextFile(fb);
   
    Vector va= new Vector(FormatOp1D.stringToDouble(jj.tab.getColumn(0)));
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    File[] afs= dd.listFiles();

    HashMap<String, GenomicRegion> idreg= new HashMap<>();
    ReadTable rt= new ReadTable(pf);
    rt.setSkipRows(0);
    Table<String> tab= rt.getTable();
    for( int i=0; i<tab.getRowNumber(); i++ ){
        ArrayList<String> r= tab.getRow(i);
        String reg= r.get(9);
        if(!reg.equals("")){
            GenomicRegion gr= GenomicRegion.parseGenomicRegoinUCSC(reg);
            idreg.put(r.get(0), gr);
            //System.out.println(r.get(0)+"   "+ gr.toUCSCFormat());
        }
    }
   


    for( int i=0; i<afs.length; i++ ){
        File af= afs[i];
        if(FileName.getExt(af).equals("txt")){
            ReadTable rtaf= new ReadTable(af);
            rtaf.setSkipRows(0);
            HashMap<String,String> idvals= rtaf.getHashMap(0, 1);
            HashMap<String,Double> idval= new HashMap<>();
            Iterator<String> it= idvals.keySet().iterator();
            while(it.hasNext()){
                String id= it.next();
                idval.put(id, Double.parseDouble(idvals.get(id)));
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    return ret;
}
   

private Tab tab(File f)throws Exception{
    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("(", "");
View Full Code Here
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protected void init() throws Exception{
    HashMap<String,Double> idv= new HashMap<>();
    String[][] arr= new ReadTable(bed).getTableAsArray();
    for( int i=0; i<arr.length ; i++ ){
        String[] r= arr[i];
        idv.put(r[3], Double.parseDouble(r[4]));
    }
    cl= new ClassifierGeneValue(idv, tag, n);
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    BedGraphExporter.writeTitle(bw, tit+"_res"+res);
    for( int i=0; i<fs.size() ; i++ ){
        File f= fs.get(i);
        System.out.println(f);
        String chr= FileName.getBaseName(f);
        String[][] arr= new ReadTable(f).getTableAsArray();
        LandscapeBuilder lb= new LandscapeBuilder();
        int pp=0; double pv=0;
        for( int j=0; j<arr.length ; j++ ){
            String[] r= arr[j];
            int p= Integer.parseInt(r[0]);
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protected void init() throws Exception{
    sets.add(new GeneSet(tag+"_"+NON));
    sets.add(new GeneSet(tag+"_"+U));
    sets.add(new GeneSet(tag+"_"+D));

    String[] ids= new ReadTable(fu).getColumn(3);
    double[] vus= FormatOp1D.objToDouble(new ReadTable(fu).getColumn(4));
    double[] vds= FormatOp1D.objToDouble(new ReadTable(fd).getColumn(4));
    for(int i=0; i<ids.length ; i++){
        String id= ids[i];
        double vu= vus[i], vd= vds[i];
        if(vu>vd){
            double diff= vu-vd;
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    File f= new File("/home/forksapien/mystudy/phd/files/temp2/list.txt"); int col=0;
    //File f= new File("/home/forksapien/mystudy/phd/files/temp2/772-wt_sense.bed"); int col=3;
    String tab= "xuhistone";


    List li =Arrays.asList(new ReadTable(f).getColumn(col));
    InspectSetAll in= new InspectSetAll(li, tab);
   
   
   
   
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protected void init() throws IOException{
    ta= new ArrayList<>();
    tl= new ArrayList<>();
    String[][] arr= new ReadTable(f).getTableAsArray();
    for( int i=0; i<arr.length ; i++ ){
        String[] r= arr[i];
        if(r.length>4){
            String id= r[0];
            String clas= r[4];
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