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

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

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}
   

protected int getNum(File sum)throws Exception {
    int n=0;
    ReadTable rt= new ReadTable(sum);
    String[] ants= rt.getColumn(4);
    for( int j=0; j<ants.length; j++ ){
        if(ants[j].equals("as")){
            n++;
        }
    }
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        init();
    }
   
   
protected void init() throws Exception{
    ReadTable rt= new ReadTable(f);
    rt.param().setSkipSyntax("#");
    rt.setSkipRows(0);
    String[][] arr= rt.getTableAsArray();
    ids= FormatOp1D.strToArrayList( rt.getColumn(0) );
    vs= FormatOp1D.doubleToArrayDouble( FormatOp1D.objToDouble(rt.getColumn(1)) );
}
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        this.std=std;
        init();
    }
protected void init() throws Exception{
    GenomicRegionsBuilder gba= new BedReader(anno).getGenomicRegionsBuilder();
    String[][] arr= new ReadTable(probe).getTableAsArray();
    double pp=-1; String pc="", pid=""; int ind=0;
    for(int i=0; i<arr.length ; i++){
        String[] r= arr[i];
        if(r[2].equalsIgnoreCase(std)){
            String id= r[0];
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    }
}
   
   
public void initRows(File f) throws IOException{
    ReadTable rt= new ReadTable(f);
    String[] rns= rt.getColumn(3);
    for(int j=0; j<rns.length ; j++){
        String rn= rns[j];
        if(!tab.containsRow(rn)){
            tab.appendEmptyRow(rn);
        }
    }
    String[][] arr= rt.getTableAsArray();
    tab.appendEmptyColumn("pos");
    tab.appendEmptyColumn("chr");
    tab.appendEmptyColumn("low");
    tab.appendEmptyColumn("high");
    tab.appendEmptyColumn("std");
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}
   
   
public void addBedFile(File f) throws Exception{
    String cn= FileName.getBaseName(f);
    ReadTable rt= new ReadTable(f);
    this.addHashMapIDToVal(rt.getHashMap(3, 4), cn);
}
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* @param f
* @throws Exception
*/
public void addTextFile(File f)throws Exception {
    String cn= FileName.getBaseName(f);
    ReadTable rt= new ReadTable(f);
    this.addHashMapIDToVal(rt.getHashMap(0, 1), cn);
}
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        }
    }
}

public void addTextFileChunk(File f)throws Exception {
    ReadTable rt= new ReadTable(f);
    ArrayList<String> r0= rt.getTable().getRow(0);
    rt= new ReadTable(f);
    rt.param().setSkipRows(0);
    for( int i=1; i<r0.size(); i++ ){
        String cn= r0.get(i).replace(" ", "");
        this.addHashMapIDToVal(rt.getHashMap(0, i), cn);
    }
}
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    File d= new File("/home/forksapien/Desktop");
    File tab= new File(d+"/combine.txt");
    File list= new File(d+"/down.txt");
   
    String[] ids= new ReadTable(list).getColumn(0);
   
   
    String tit= "row";
    ArrayList<String> idsa= new ArrayList<>();
    idsa.add(tit);
    for(int i=0; i<ids.length ; i++){
        idsa.add(ids[i]);
    }
   
   
    ReadTable rt= new ReadTable(tab);
    Table<String> table= new Table<>(rt.getTableAsArray());
   
    GrepTable gt= new GrepTable(table,0);
   
    gt.grep(idsa).writeToFile(new File(list.getParentFile()+"/all_"+FileName.getBaseName(list)+".txt"));
   
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    File out = new File(list.getParentFile()+"/out_"+list.getName());
   
    File nmf= new File(dir+"/anno/sgd_name.bed");
   
   
    HashMap<String,String> nn= new ReadTable(nmf).getHashMap(3, 4);
    ReadTable rt1= new ReadTable(new File(dir+"/data/rna/norm/score/sacCer1-xu/772-wt_r1_sense.bed"));
    ReadTable rt2= new ReadTable(new File(dir+"/data/rna/norm/score/sacCer1-xu/773-zd_r1_sense.bed"));
    HashMap<String,String>[] vs= new HashMap[]{
        rt1.getHashMap(3, 4),rt2.getHashMap(3, 4),
    };
   
    NamedTable<String,String,String> tt= new NamedTable<>();
    String[] ns= new ReadTable(list).getColumn(0);
    Arrays.sort(ns);
    for(int i=0; i<ns.length ; i++){
        tt.appendEmptyRow(ns[i]);
    }
   
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protected void init() throws IOException, RegionException{
    hm= new HashMap<>();
    ReadTable rt= new ReadTable(f);
    rt.param().setSkipRows(0);
    String[][] arr= rt.getTableAsArray();
    for( int i=0; i<arr.length ; i++ ){
        String[] r= arr[i];
        r[6]= r[6].replaceAll(" ", "");
        String id= r[6].split(",")[0];
        String type= r[5];
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