Ejemplo n.º 1
0
  /*.................................................................................................................*/
  public void processAceFileWithContig(
      CharacterData data,
      MesquiteModule ownerModule,
      String processedAceFilePath,
      String fragmentDirPath,
      AceFile ace,
      SequenceUploader uploader,
      String geneName,
      MesquiteString fullName,
      String baseName,
      MesquiteString voucherCode,
      int it) {
    DNAData editedData = ChromaseqUtil.getEditedData(data);
    DNAData originalData = ChromaseqUtil.getOriginalData(data);
    Taxa taxa = data.getTaxa();
    ace.setNameTranslation(fileNameTranslation);
    ownerModule.log(ace.contigListForLog() + StringUtil.lineEnding());
    if (processPolymorphisms) ace.processPolys(); // creates an additional CO that has polys in it
    if (renameContigsInAceFiles) ace.renameContigs(fullName.toString(), addFragName, geneName);
    ace.setLowQualityToLowerCase(qualThresholdForLowerCase);
    ace.writeToPropertiesFile(contigPropertiesFileBuffer, fullName.toString());
    if (truncateMixedEnds)
      ace.trimMixedEnds(mixedEndThreshold, mixedEndWindow, qualThresholdForTrim, addPhrapFailures);

    /*		if (uploadResultsToDatabase && StringUtil.notEmpty(databaseURL)) {
    			uploader.uploadAceFileToServer(MesquiteXMLToLUtilities.getTOLPageDatabaseURL(databaseURL), ace, processPolymorphisms, qualThresholdForTrim);
    		}
    */
    System.out.println("\n\nfasta file name: " + baseName + " ace file: " + ace);
    MesquiteFile.putFileContents(
        fragmentDirPath
            + MesquiteFile.fileSeparator
            + ChromaseqUtil.processedFastaFolder
            + MesquiteFile.fileSeparator
            + baseName
            + ".fas",
        ace.toFASTAString(processPolymorphisms, qualThresholdForTrim),
        true);
    MesquiteFile.putFileContents(processedAceFilePath, ace.toString(processPolymorphisms), true);
    ace.importSequence(
        taxa,
        editedData,
        it,
        originalData,
        ChromaseqUtil.getQualityData(data),
        ChromaseqUtil.getRegistryData(data),
        singleTaxaBlock,
        processPolymorphisms,
        maxChar,
        " contig ",
        false,
        voucherCode);
  }
Ejemplo n.º 2
0
 /*.................................................................................................................*/
 String getComDelim() {
   if (externalProcRunner.isWindows()) return ";" + StringUtil.lineEnding();
   else return ";" + StringUtil.lineEnding();
 }
Ejemplo n.º 3
0
  /*.................................................................................................................*/
  void formCommandFile(String dataFileName, int firstOutgroup) {
    if (parallel) {
      commands = "";
    }
    commands += getTNTCommand("mxram " + mxram);

    commands += getTNTCommand("report+0/1/0");
    commands += getTNTCommand("log " + logFileName);
    commands += getTNTCommand("p " + dataFileName);
    commands += getTNTCommand("vversion");
    if (MesquiteInteger.isCombinable(firstOutgroup) && firstOutgroup >= 0)
      commands += getTNTCommand("outgroup " + firstOutgroup);
    if (bootstrapOrJackknife()) {
      if (parallel) {
        commands += indentTNTCommand("ptnt begin parallelRun " + numSlaves + "/ram x 2 = ");
      }
      if (StringUtil.notEmpty(bootSearchScriptPath)) {
        String script = MesquiteFile.getFileContentsAsString(bootSearchScriptPath);
        if (StringUtil.notEmpty(script)) commands += script;
      } else
        commands += StringUtil.lineEnding() + bootstrapSearchArguments + StringUtil.lineEnding();
      String saveTreesString = "";
      if (resamplingAllConsensusTrees) saveTreesString = " savetrees ";
      String bootSearchString = " [xmult; bb]";
      bootSearchString = "";

      if (parallel) {
        int numRepsPerSlave = bootstrapreps / numSlaves;
        if (numRepsPerSlave * numSlaves < bootstrapreps) numRepsPerSlave++;
        if (searchStyle == BOOTSTRAPSEARCH)
          commands +=
              getTNTCommand(
                  "resample boot cut 50 "
                      + saveTreesString
                      + " replications "
                      + numRepsPerSlave
                      + " [xmult; bb] savetrees"); // + getComDelim();
        else if (searchStyle == JACKKNIFESEARCH)
          commands +=
              getTNTCommand(
                  "resample jak cut 50 "
                      + saveTreesString
                      + " replications "
                      + numRepsPerSlave
                      + " [xmult; bb] savetrees"); // + getComDelim();
        else if (searchStyle == SYMSEARCH)
          commands +=
              getTNTCommand(
                  "resample sym cut 50 "
                      + saveTreesString
                      + " replications "
                      + numRepsPerSlave
                      + " [xmult; bb] savetrees"); // + getComDelim();
        else if (searchStyle == POISSONSEARCH)
          commands +=
              getTNTCommand(
                  "resample poisson cut 50 "
                      + saveTreesString
                      + " replications "
                      + numRepsPerSlave
                      + " [xmult; bb] savetrees"); // + getComDelim();
        commands += getTNTCommand("return");
        commands += getTNTCommand("ptnt wait parallelRun");
        commands += getTNTCommand("ptnt get parallelRun");
      } else {
        if (!resamplingAllConsensusTrees) {
          commands += getTNTCommand("macro=");
          commands += getTNTCommand("ttags =");
        }
        commands += getTNTCommand("tsave *" + treeFileName);
        if (bootstrapAllowed) {
          if (searchStyle == BOOTSTRAPSEARCH)
            commands +=
                getTNTCommand(
                    "resample boot "
                        + saveTreesString
                        + " replications "
                        + bootstrapreps
                        + bootSearchString); // + getComDelim();
          else if (searchStyle == JACKKNIFESEARCH)
            commands +=
                getTNTCommand(
                    "resample jak cut 50 "
                        + saveTreesString
                        + " replications "
                        + bootstrapreps
                        + bootSearchString); // + getComDelim();
          else if (searchStyle == SYMSEARCH)
            commands +=
                getTNTCommand(
                    "resample sym cut 50 "
                        + saveTreesString
                        + " replications "
                        + bootstrapreps
                        + bootSearchString); // + getComDelim();
          else if (searchStyle == POISSONSEARCH)
            commands +=
                getTNTCommand(
                    "resample poisson cut 50 "
                        + saveTreesString
                        + " replications "
                        + bootstrapreps
                        + bootSearchString); // + getComDelim();
        }
        if (!resamplingAllConsensusTrees) commands += getTNTCommand("save *");
        else commands += getTNTCommand("save");
        commands += getTNTCommand("tsave/");
        if (!resamplingAllConsensusTrees) {
          commands += getTNTCommand("ttags -/");
          commands += getTNTCommand("macro-");
        }
      }

      // commands += getTNTCommand("proc/") ;

      commands += getTNTCommand("log/");

      //	if (!parallel)
      commands += getTNTCommand("quit");
    } else {
      // commands += getTNTCommand("tsave !5 " + treeFileName) ;   // if showing intermediate trees
      commands += getTNTCommand("tsave *" + treeFileName);
      if (StringUtil.notEmpty(searchScriptPath)) {
        String script = MesquiteFile.getFileContentsAsString(searchScriptPath);
        if (StringUtil.notEmpty(script)) commands += script;
      } else commands += searchArguments;
      commands += otherOptions;
      if (harvestOnlyStrictConsensus) commands += getTNTCommand("nelsen *");
      commands += getTNTCommand("save");
      commands += getTNTCommand("log/");

      commands += getTNTCommand("tsave/");
      commands += getTNTCommand("quit");
    }
  }