Examples of gem.parser.TabDelimitedFileParser

gem.parser.TabDelimitedFileParser
Generic tab-delimited file parser useful only when you are interested in two of the columns. @author Ozgun BaburDate: Apr 15, 2008 Time: 11:35:20 AM

  }


  public static void main(String[] args) throws IOException
  {
    String facName = "AR";
    TabDelimitedFileParser parser = new TabDelimitedFileParser("resource/factors/"+ facName + "_andr.txt");
    Set<String> tarNames = parser.getColumnSet("Target");
    System.out.println("tarNames.size() = " + tarNames.size());
    
    List<Tuple> tuples = new ArrayList<Tuple>();


    for (String tarName : tarNames)

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  public static Map<String, Gene> readMouseHomologs(Set<String> humanids, String dir,
    double minvar, double minvarlog) throws IOException
  {
    System.out.println("initial size = " + humanids.size());
    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/human2mouse.txt");
    Map<String, String> hum2mouStr = p.getOneToOneMap("Human", "Mouse");


    Map<String, List<String>> hum2mous = new HashMap<String, List<String>>();
    Map<String, List<String>> mou2hums = new HashMap<String, List<String>>();
    for (String hum : hum2mouStr.keySet())
    {

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  }


  public static Map<String, double[]> readSubset(Set<String> egids, String dir,
    double minvar, double minVarLog) throws IOException
  {
    TabDelimitedFileParser parser = new TabDelimitedFileParser(dir + "/platform.txt");
    Map<String, Set<String>> eg2id = parser.getOneToManyMap("ENTREZ_GENE_ID", "ID");


    for (String eg : new HashSet<String>(eg2id.keySet()))
    {
      if (eg.contains("/"))
      {

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//    Map<String, String> id2sym = p.getOneToOneMap("ID", "Gene Symbol");


    Map<String, String> g2s = Triplet.getGeneToSymbolMap();


//    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/factors/AR-select-small.txt");
    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/NuclearReceptors.txt");
    Set<String> syms = p.getColumnSet(0);


    BufferedReader reader = new BufferedReader(new FileReader(dir + "data.txt"));


    int i = 0;
    for (String line = reader.readLine(); line != null; line = reader.readLine())

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  }


  private static void test3() throws IOException
  {
    TabDelimitedFileParser parser = new TabDelimitedFileParser("resource/factors/AR_andr.txt");
    Map<String, String> score = parser.getOneToOneMap("Target", "Score");


    parser = new TabDelimitedFileParser("resource/factors/AR-select.txt");
    Set<String> select = parser.getColumnSet(0);


    List<String> up = new ArrayList<String>();
    List<String> dw = new ArrayList<String>();


    for (String s : select)

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    printClassCounts(map);
  }


  private static List<Triplet> filterToSign(List<Triplet> trips, int sign)
  {
    TabDelimitedFileParser parser = new TabDelimitedFileParser("resource/factors/AR_andr.txt");
    Map<String, String> score = parser.getOneToOneMap("Target", "Score");


    List<Triplet> list = new ArrayList<Triplet>();


    for (Triplet t : trips)
    {

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    String[] types = new String[]{
      ENHANCES_ACTIVATION, ATTENUATES_ACTIVATION, INVERTS_ACTIVATION,    XOR_ACTIVATE, OR_ACTIVATE, FMOD_ACTIVATE,
      ENHANCES_INHIBITION, ATTENUATES_INHIBITION, INVERTS_INHIBITION,   XOR_INHIBIT, OR_INHIBIT, FMOD_INHIBIT,
      MOA_INSIGNIFICANT};


    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/factors/AR_andr_small.txt");
    Map<String, String> score = p.getOneToOneMap("Target", "Score");


    List<String> names = getSortedNames(map.keySet());
    TermCounter tc = new TermCounter();


    for (String name : names)

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  }
  
  public static void findActivityInOtherTissue() throws Throwable
  {
//    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/factors/AR-select-small.txt");
    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/NuclearReceptors.txt");
    Set<String> tarNames = p.getColumnSet(0);
    tarNames.add("AR");
    Set<String> tarIDs = IDUtil.covertSym2Gene(tarNames);
    String dir = "resource/expdata/expo/";
    Map<String, Gene> geneMap = ExpDataReader.readGenes(tarIDs, dir, 0, 0);
    boolean[][] pos = StageAnalyzer.getPos(dir);
    String[] stgNm = StageAnalyzer.getStageNames(dir);
    int indBr = ArrayUtils.getIndexOf(stgNm, "Breast");
    int indPr = ArrayUtils.getIndexOf(stgNm, "Prostate");


    List<Gene> genes = Gene.sortWithSym(geneMap.values());
    Gene ar = genes.get(5);
    int cnt = 0;
    tarNames.clear();
    for (Gene g : genes)
    {
      g.takeLog();
      double globMean = g.calcMean();
      double meanPr = g.calcMean(pos[indPr]);
      double meanBr = g.calcMean(pos[indBr]);
      double varBr = g.calcVariance(pos[indBr]);
      boolean select = meanBr > globMean && varBr > 1;
      
      double cor = Pearson.calcCorrelation(g.value, ar.value, pos[indBr]);


      if (select)
      {
        System.out.println(g.getSymbol() + "\t" + globMean + "\t" +
          meanPr + "\t" + meanBr + "\t" + varBr + "\t" + cor);
        cnt++;
        tarNames.add(g.getSymbol());
      }
    }
    System.out.println("cnt = " + cnt);


    p = new TabDelimitedFileParser("resource/NuclearReceptors.txt");
    Set<String> nucres = p.getColumnSet(0);
//    TripletMaker.make("AR", HPRDParser.readFor(Collections.singleton("AR")).get("AR"), tarNames,
//    TripletMaker.make("AR", nucres, tarNames,
//      "resource/tartrips/breast-AR-trips.txt");


    Map<String, Gene> symMap = Gene.getSymMap(genes);

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//    String dir = "resource/expdata/GSE1133-GPL96/";
//    String dir = "resource/expdata/GSE13159/";
//    String dir = "resource/expdata/GSE7307/";
    String dir = "resource/expdata/expo_select/";
    TabDelimitedFileParser parser = new TabDelimitedFileParser(dir + "platform.txt");
    Map<String, String> id2sym = parser.getOneToOneMap("ID", "Gene Symbol");


    parser = new TabDelimitedFileParser("resource/phospho-site/ModifCounts.txt");
    Map<String, String> sym2modif = parser.getOneToOneMap("Gene", "ModifCnt");


    String[] tisIndex = getTissueIndexes();


//    Progress prg = new Progress(54675);
    Progress prg = new Progress(19800);

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    String[] expNames = firstLine.split("\t");
    for (int i = 0; i < expNames.length; i++)
    {
      expNames[i] = expNames[i].substring(1, expNames[i].length() - 1);
    }
    TabDelimitedFileParser parser = new TabDelimitedFileParser("resource/celltypes_expO.txt");
    Map<String, String> exp2tiss = parser.getOneToOneMap("Sample", "Tissue");


    for (String exp : new HashSet<String>(exp2tiss.keySet()))
    {
//      exp2tiss.put(exp, exp2tiss.get(exp).substring(0, exp2tiss.get(exp).indexOf(" ")).toLowerCase());
      exp2tiss.put(exp, exp2tiss.get(exp).toLowerCase());

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Related Classes of gem.parser.TabDelimitedFileParser

gem.ActivityPredicter

gem.ActivityPredicter3

gem.CellLineCorrecter

gem.CellTypeMatcher

gem.ClusterAnalyzer

gem.ClusterAnalyzer2

gem.CrossPlatformMapper

gem.ExpDataReader

gem.GEMAllPairs

gem.GRARAnalyzer

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