Example #1
0
  ExitCodes main_(int, const char**)
  {
    // LOG_DEBUG << "Starting..." << endl;

    //----------------------------------------------------------------
    // load ids
    //----------------------------------------------------------------
    // LOG_DEBUG << "Loading idXML..." << endl;
    String id = getStringOption_("id");
    vector<ProteinIdentification> protein_ids;
    vector<PeptideIdentification> peptide_ids;
    FileTypes::Type in_type = FileHandler::getType(id);
    if (in_type == FileTypes::IDXML)
    {
      IdXMLFile().load(id, protein_ids, peptide_ids);
    }
    else if (in_type == FileTypes::MZIDENTML)
    {
      MzIdentMLFile().load(id, protein_ids, peptide_ids);
    }
    else
    {
      throw Exception::IllegalArgument(__FILE__, __LINE__,
                                       __PRETTY_FUNCTION__,
                                       "wrong id fileformat");
    }

    String in = getStringOption_("in");
    String out = getStringOption_("out");
    in_type = FileHandler::getType(in);
    //----------------------------------------------------------------
    //create mapper
    //----------------------------------------------------------------
    // LOG_DEBUG << "Creating mapper..." << endl;
    IDMapper mapper;
    Param p = mapper.getParameters();
    p.setValue("rt_tolerance", getDoubleOption_("rt_tolerance"));
    p.setValue("mz_tolerance", getDoubleOption_("mz_tolerance"));
    p.setValue("mz_measure", getStringOption_("mz_measure"));
    p.setValue("mz_reference", getStringOption_("mz_reference"));
    p.setValue("ignore_charge", getFlag_("ignore_charge") ? "true" : "false");
    mapper.setParameters(p);

    //----------------------------------------------------------------
    // consensusXML
    //----------------------------------------------------------------
    if (in_type == FileTypes::CONSENSUSXML)
    {
      // LOG_DEBUG << "Processing consensus map..." << endl;
      ConsensusXMLFile file;
      ConsensusMap map;
      file.load(in, map);

      bool measure_from_subelements = getFlag_("consensus:use_subelements");
      bool annotate_ids_with_subelements = getFlag_("consensus:annotate_ids_with_subelements");

      mapper.annotate(map, peptide_ids, protein_ids, measure_from_subelements, annotate_ids_with_subelements);

      //annotate output with data processing info
      addDataProcessing_(map, getProcessingInfo_(DataProcessing::IDENTIFICATION_MAPPING));

      file.store(out, map);
    }

    //----------------------------------------------------------------
    // featureXML
    //----------------------------------------------------------------
    if (in_type == FileTypes::FEATUREXML)
    {
      // LOG_DEBUG << "Processing feature map..." << endl;
      FeatureMap map;
      FeatureXMLFile file;
      file.load(in, map);

      mapper.annotate(map, peptide_ids, protein_ids,
                      getFlag_("feature:use_centroid_rt"),
                      getFlag_("feature:use_centroid_mz"));

      //annotate output with data processing info
      addDataProcessing_(map, getProcessingInfo_(DataProcessing::IDENTIFICATION_MAPPING));

      file.store(out, map);
    }

    //----------------------------------------------------------------
    // MzQuantML
    //----------------------------------------------------------------
    if (in_type == FileTypes::MZQUANTML)
    {
      // LOG_DEBUG << "Processing mzq ..." << endl;
      MSQuantifications msq;
      MzQuantMLFile file;
      file.load(in, msq);

      bool measure_from_subelements = getFlag_("consensus:use_subelements");
      for (std::vector<ConsensusMap>::iterator it = msq.getConsensusMaps().begin(); it != msq.getConsensusMaps().end(); ++it)
      {
        mapper.annotate(*it, peptide_ids, protein_ids, measure_from_subelements);
        //annotate output with data processing info
        addDataProcessing_(*it, getProcessingInfo_(DataProcessing::IDENTIFICATION_MAPPING));
      }

      //~ writeDebug_(msq.getConsensusMaps().size(),3);
      //~ writeDebug_(msq.getConsensusMaps().back().size(),3);
      //~ writeDebug_(msq.getAnalysisSummary().quant_type_,3);
      file.store(out, msq);
    }

    // LOG_DEBUG << "Done." << endl;
    return EXECUTION_OK;
  }
  ExitCodes main_(int, const char**)
  {
    //input file names
    String in = getStringOption_("in");
    String out = getStringOption_("out");
    String out_mzq = getStringOption_("out_mzq");

    //prevent loading of fragment spectra
    PeakFileOptions options;
    options.setMSLevels(vector<Int>(1, 1));

    //reading input data
    MzMLFile f;
    f.getOptions() = options;
    f.setLogType(log_type_);

    PeakMap exp;
    f.load(in, exp);
    exp.updateRanges();

    if (exp.getSpectra().empty())
    {
      throw OpenMS::Exception::FileEmpty(__FILE__, __LINE__, __FUNCTION__, "Error: No MS1 spectra in input file.");
    }

    // determine type of spectral data (profile or centroided)
    SpectrumSettings::SpectrumType  spectrum_type = exp[0].getType();

    if (spectrum_type == SpectrumSettings::RAWDATA)
    {
      if (!getFlag_("force"))
      {
        throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Error: Profile data provided but centroided spectra expected. To enforce processing of the data set the -force flag.");
      }
    }

    //load seeds
    FeatureMap seeds;
    if (getStringOption_("seeds") != "")
    {
      FeatureXMLFile().load(getStringOption_("seeds"), seeds);
    }

    //setup of FeatureFinder
    FeatureFinder ff;
    ff.setLogType(log_type_);

    // A map for the resulting features
    FeatureMap features;

    // get parameters specific for the feature finder
    Param feafi_param = getParam_().copy("algorithm:", true);
    writeDebug_("Parameters passed to FeatureFinder", feafi_param, 3);

    // Apply the feature finder
    ff.run(FeatureFinderAlgorithmPicked::getProductName(), exp, features, feafi_param, seeds);
    features.applyMemberFunction(&UniqueIdInterface::setUniqueId);

    // DEBUG
    if (debug_level_ > 10)
    {
      FeatureMap::Iterator it;
      for (it = features.begin(); it != features.end(); ++it)
      {
        if (!it->isMetaEmpty())
        {
          vector<String> keys;
          it->getKeys(keys);
          LOG_INFO << "Feature " << it->getUniqueId() << endl;
          for (Size i = 0; i < keys.size(); i++)
          {
            LOG_INFO << "  " << keys[i] << " = " << it->getMetaValue(keys[i]) << endl;
          }
        }
      }
    }

    //-------------------------------------------------------------
    // writing files
    //-------------------------------------------------------------

    //annotate output with data processing info
    addDataProcessing_(features, getProcessingInfo_(DataProcessing::QUANTITATION));

    // write features to user specified output file
    FeatureXMLFile map_file;

    // Remove detailed convex hull information and subordinate features
    // (unless requested otherwise) to reduce file size of feature files
    // unless debugging is turned on.
    if (debug_level_ < 5)
    {
      FeatureMap::Iterator it;
      for (it = features.begin(); it != features.end(); ++it)
      {
        it->getConvexHull().expandToBoundingBox();
        for (Size i = 0; i < it->getConvexHulls().size(); ++i)
        {
          it->getConvexHulls()[i].expandToBoundingBox();
        }
        it->getSubordinates().clear();
      }
    }

    map_file.store(out, features);

    if (!out_mzq.trim().empty())
    {
      MSQuantifications msq(features, exp.getExperimentalSettings(), exp[0].getDataProcessing());
      msq.assignUIDs();
      MzQuantMLFile file;
      file.store(out_mzq, msq);
    }

    return EXECUTION_OK;
  }
Example #3
0
  ExitCodes main_(int, const char **)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    String in = getStringOption_("in");
    String out = getStringOption_("out");
    String out_stats = getStringOption_("out_stats");
    String out_mzq = getStringOption_("out_mzq");

    Int itraq_type = (getStringOption_("type") == "4plex" ? ItraqQuantifier::FOURPLEX : ItraqQuantifier::EIGHTPLEX);
    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------

    MzMLFile mz_data_file;
    MSExperiment<Peak1D> exp;
    mz_data_file.setLogType(log_type_);
    mz_data_file.load(in, exp);

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------
    Param extract_param(getParam_().copy("algorithm:Extraction:", true));
    ItraqChannelExtractor itraq_ce(itraq_type, extract_param);

    ConsensusMap consensus_map_raw, consensus_map_quant;
    // extract raw signals
    itraq_ce.run(exp, consensus_map_raw);

    // do normalization
    Param quant_param(getParam_().copy("algorithm:Quantification:", true));
    ItraqQuantifier itraq_quant(itraq_type, quant_param);

    itraq_quant.run(consensus_map_raw, consensus_map_quant);

    // assign unique ID to output file (this might throw an exception.. but thats ok, as we want the program to quit then)
    if (getStringOption_("id_pool").trim().length() > 0) getDocumentIDTagger_().tag(consensus_map_quant);

    // annotate output file with MetaInformation
    Param metainfo_param(getParam_().copy("algorithm:MetaInformation:", true));
    for (Param::ParamIterator it = metainfo_param.begin(); it != metainfo_param.end(); ++it)
    {
      consensus_map_quant.setMetaValue(it->name, it->value);
    }


    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------

    //annotate output with data processing info
    addDataProcessing_(consensus_map_quant, getProcessingInfo_(DataProcessing::QUANTITATION));

    // add filename references
    for (ConsensusMap::FileDescriptions::iterator it = consensus_map_quant.getFileDescriptions().begin();
         it != consensus_map_quant.getFileDescriptions().end();
         ++it)
    {
      it->second.filename = in;
    }

    ConsensusXMLFile cm_file;
    cm_file.store(out, consensus_map_quant);

    if (!out_mzq.trim().empty())
    {
      MSQuantifications msq;
      std::vector<std::vector<std::pair<String, DoubleReal> > > labels;
      if (itraq_type == ItraqQuantifier::FOURPLEX)
      {
        for (Size i = 0; i < 4; ++i)
        {
          std::vector<std::pair<String, DoubleReal> > one_label;
          one_label.push_back(std::make_pair<String, DoubleReal>(String("Channel ") + String(ItraqConstants::CHANNELS_FOURPLEX[i][0]), DoubleReal(ItraqConstants::CHANNELS_FOURPLEX[i][0])));
          labels.push_back(one_label);
        }
      }
      else       //ItraqQuantifier::EIGHTPLEX
      {
        for (Size i = 0; i < 8; ++i)
        {
          std::vector<std::pair<String, DoubleReal> > one_label;
          one_label.push_back(std::make_pair<String, DoubleReal>(String("Channel ") + String(ItraqConstants::CHANNELS_EIGHTPLEX[i][0]), DoubleReal(ItraqConstants::CHANNELS_EIGHTPLEX[i][0])));
          labels.push_back(one_label);
        }
      }
      msq.registerExperiment(exp, labels);       //add assays
      msq.assignUIDs();
      MSQuantifications::QUANT_TYPES quant_type = MSQuantifications::MS2LABEL;
      msq.setAnalysisSummaryQuantType(quant_type);      //add analysis_summary_

      msq.addConsensusMap(consensus_map_quant);      //add ITRAQAnalyzer result
      //~ add AuditCollection - no such concept in TOPPTools yet
      MzQuantMLFile file;
      file.store(out_mzq, msq);
    }

    std::cout << itraq_quant.getStats();
    if (!out_stats.trim().empty())
    {
      ofstream f;
      f.open(out_stats.c_str(), ios_base::out);
      f << itraq_quant.getStats();
      f.close();
    }

    return EXECUTION_OK;
  }