Package gem.parser

Examples of gem.parser.TabDelimitedFileParser

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  {
    Map<String,Set<String>> map =
      HPRDParser.readFor(new HashSet<String>(Arrays.asList(FACNAME)));
    Set<String> interactors = map.get(FACNAME);

    TabDelimitedFileParser parser =
      new TabDelimitedFileParser("resource/factors/" + FACNAME + ".txt");
    Set<String> targets = parser.getColumnSet(0);

    SetUtils.removeCommon(interactors, targets);

    // Remove ETV1-AR interaction from triplets. This is a false positive entry in HPRD. We
    // noticed it while investigating our results. GEM reported ETV1 as a strong modulator of
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//    if (factorSym.equals("ETV1")) interactors.add("KIT");
//    if (factorSym.equals("MITF")) interactors.addAll(Arrays.asList("MAP2K1", "MAP2K2", "MAPK3", "RPS6KA1", "RPS6KA2", "RPS6KA3", "HIF1", "YWHAZ", "MAPK11"));

    System.out.println("number of interacting proteins = " + interactors.size());

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

//    parser = new TabDelimitedFileParser("resource/factors/" + factorSym + "_andr.txt");
//    Set<String> confirmed = parser.getColumnSet(0);
//    confirmed.removeAll(interactors);
    interactors.removeAll(targets);
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    Set<String> interactors = new HashSet<String>(Arrays.asList(mod));
    interactors.add(factorSym);

    System.out.println("number of interacting proteins = " + interactors.size());

    TabDelimitedFileParser parser =
      new TabDelimitedFileParser("resource/factors/" + factorSym + ".txt");

    Set<String> targets = parser.getColumnSet(0);

    System.out.println("number of targets = " + targets.size());

    List<String> trips = new ArrayList<String>();
    for (String fac : interactors)
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  private static void prepare(String factorSym, String modSym) throws Throwable
  {
    Set<String> interactors = new HashSet<String>();
    interactors.add(modSym);

    TabDelimitedFileParser parser =
      new TabDelimitedFileParser("resource/factors/" + factorSym + ".txt");

    Set<String> targets = parser.getColumnSet(0);

    if (targets.contains(modSym)) System.out.println(modSym + " is also a target");
    targets.removeAll(interactors);

    System.out.println("number of targets = " + targets.size());
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    writeTrips(make("AR", new HashSet<String>(mods), targets), "resource/" + "NR3C1" + "-AR-trips.txt");
  }

  private static Set<String> getARTargets_ChEA()
  {
    TabDelimitedFileParser parser = new TabDelimitedFileParser("resource/AR_tars.txt");
    Set<String> targets = parser.getColumnSet("AR Targets");
    return targets;
  }
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  }

  private static List<Triplet> filterTars(List<Triplet> trips)
  {
    String file = "resource/factors/temp";
    TabDelimitedFileParser parser = new TabDelimitedFileParser(file);
    Set<String> tars = parser.getColumnSet(3);
    List<Triplet> list = new ArrayList<Triplet>();

    for (Triplet t : trips)
    {
      if (tars.contains(t.getTSym())) list.add(t);
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  public static final int MODULE_SIZE_THR = 5;
  public static final int AVG_BINS_PER_GENE = 5;

  public static void main(String[] args) throws Throwable
  {
    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/factors/AR-select-small.txt");
    Set<String> tarSym = p.getColumnSet(0);

    List<String> modList = getModSymSet();
//    modList.removeAll(tarSym);
//    modList.add("KLK3");
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  }

  private static int[] getSigns(Gene[] genes)
  {
    int[] signs = new int[genes.length];
    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/factors/AR_andr_small.txt");
    Map<String, String> score = p.getOneToOneMap("Target", "Score");
    for (int i = 0; i < genes.length; i++)
    {
      signs[i] = score.get(genes[i].getSymbol()).startsWith("-") ? -1 : 1;
    }
    return signs;
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  //---------------------------------------------------------------------------------------------|

  public static void printResistanceGeneEnrichment(Gene[] tar, Gene[] mod, int[] sign)
  {
    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/factors/AR-resistance.txt");
    Set<String> resSet = p.getColumnSet(0);
    Map<Gene, Set<String>> corMap = new HashMap<Gene, Set<String>>();
    for (int i = 0; i < mod.length; i++)
    {
      for (int j = 0; j < tar.length; j++)
      {
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    }
  }

  public static List<Gene> getGRResponseModule(Gene[] tars)
  {
    TabDelimitedFileParser p = new TabDelimitedFileParser("resource/resistance_resp1.txt");
    Set<String> resp = p.getColumnSet(0);
    List<Gene> list = new ArrayList<Gene>();

    for (Gene tar : tars)
    {
      if (resp.contains(tar.getSymbol())) list.add(tar);
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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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