예제 #1
0
  void EDTAFile::store(const String& filename, const ConsensusMap& map) const
  {
    TextFile tf;

    // search for maximum number of sub-features (since this determines the number of columns)
    Size max_sub(0);
    for (Size i = 0; i < map.size(); ++i)
    {
      max_sub = std::max(max_sub, map[i].getFeatures().size());
    }

    // write header
    String header("RT\tm/z\tintensity\tcharge");
    for (Size i = 1; i <= max_sub; ++i)
    {
      header += "\tRT" + String(i) + "\tm/z" + String(i) + "\tintensity" + String(i) + "\tcharge" + String(i);
    }
    tf.addLine(header);

    for (Size i = 0; i < map.size(); ++i)
    {
      ConsensusFeature f = map[i];
      // consensus
      String entry = String(f.getRT()) + "\t" + f.getMZ() + "\t" + f.getIntensity() + "\t" + f.getCharge();
      // sub-features
      ConsensusFeature::HandleSetType handle = f.getFeatures();
      for (ConsensusFeature::HandleSetType::const_iterator it = handle.begin(); it != handle.end(); ++it)
      {
        entry += String("\t") + it->getRT() + "\t" + it->getMZ() + "\t" + it->getIntensity() + "\t" + it->getCharge();
      }
      // missing sub-features
      for (Size j = handle.size(); j < max_sub; ++j)
      {
        entry += "\tNA\tNA\tNA\tNA";
      }
      tf.addLine(entry);
    }


    tf.store(filename);
  }
예제 #2
0
  void IBSpectraFile::store(const String& filename, const ConsensusMap& cm)
  {
    // typdefs for shorter code
    typedef std::vector<ProteinHit>::iterator ProtHitIt;

    // general settings .. do we need to expose these?
    // ----------------------------------------------------------------------
    /// Allow also non-unique peptides to be exported
    bool allow_non_unique = true;
    /// Intensities below this value will be set to 0.0 to avoid numerical problems when quantifying
    double intensity_threshold = 0.00001;
    // ----------------------------------------------------------------------


    // guess experiment type
    boost::shared_ptr<IsobaricQuantitationMethod> quantMethod = guessExperimentType_(cm);

    // we need the protein identifications to reference the protein names
    ProteinIdentification protIdent;
    bool has_proteinIdentifications = false;
    if (cm.getProteinIdentifications().size() > 0)
    {
      protIdent = cm.getProteinIdentifications()[0];
      has_proteinIdentifications = true;
    }

    // start the file by adding the tsv header
    TextFile textFile;
    textFile.addLine(ListUtils::concatenate(constructHeader_(*quantMethod), "\t"));

    for (ConsensusMap::ConstIterator cm_iter = cm.begin();
         cm_iter != cm.end();
         ++cm_iter)
    {
      const ConsensusFeature& cFeature = *cm_iter;
      std::vector<IdCSV> entries;

      /// 1st we extract the identification information from the consensus feature
      if (cFeature.getPeptideIdentifications().size() == 0 || !has_proteinIdentifications)
      {
        // we store unidentified hits anyway, because the iTRAQ quant is still helpful for normalization
        entries.push_back(IdCSV());
      }
      else
      {
        // protein name:
        const PeptideHit& peptide_hit = cFeature.getPeptideIdentifications()[0].getHits()[0];
        std::set<String> protein_accessions = peptide_hit.extractProteinAccessions();
        if (protein_accessions.size() != 1)
        {
          if (!allow_non_unique) continue; // we only want unique peptides
        }

        for (std::set<String>::const_iterator prot_ac = protein_accessions.begin(); prot_ac != protein_accessions.end(); ++prot_ac)
        {
          IdCSV entry;
          entry.charge = cFeature.getPeptideIdentifications()[0].getHits()[0].getCharge();
          entry.peptide = cFeature.getPeptideIdentifications()[0].getHits()[0].getSequence().toUnmodifiedString();
          entry.theo_mass = cFeature.getPeptideIdentifications()[0].getHits()[0].getSequence().getMonoWeight(Residue::Full, cFeature.getPeptideIdentifications()[0].getHits()[0].getCharge());

          // write modif
          entry.modif = getModifString_(cFeature.getPeptideIdentifications()[0].getHits()[0].getSequence());

          ProtHitIt proteinHit = protIdent.findHit(*prot_ac);
          if (proteinHit == protIdent.getHits().end())
          {
            std::cerr << "Protein referenced in peptide not found...\n";
            continue; // protein not found
          }

          entry.accession = proteinHit->getAccession();
          entries.push_back(entry);
        }
      }

      // 2nd we add the quantitative information of the channels

      // .. skip features with 0 intensity
      if (cFeature.getIntensity() == 0)
      {
        continue;
      }

      for (std::vector<IdCSV>::iterator entry = entries.begin();
           entry != entries.end();
           ++entry)
      {
        // set parent intensity
        entry->parent_intens = cFeature.getIntensity();
        entry->retention_time = cFeature.getRT();
        entry->spectrum = cFeature.getUniqueId();
        entry->exp_mass = cFeature.getMZ();

        // create output line
        StringList currentLine;

        // add entry to currentLine
        entry->toStringList(currentLine);

        // extract channel intensities and positions
        std::map<Int, double> intensityMap;
        ConsensusFeature::HandleSetType features = cFeature.getFeatures();

        for (ConsensusFeature::HandleSetType::const_iterator fIt = features.begin();
             fIt != features.end();
             ++fIt)
        {
          intensityMap[Int(fIt->getMZ())] = (fIt->getIntensity() > intensity_threshold ? fIt->getIntensity() : 0.0);
        }
        for (IsobaricQuantitationMethod::IsobaricChannelList::const_iterator it = quantMethod->getChannelInformation().begin();
             it != quantMethod->getChannelInformation().end();
             ++it)
        {
          currentLine.push_back(String(it->center));
        }
        for (IsobaricQuantitationMethod::IsobaricChannelList::const_iterator it = quantMethod->getChannelInformation().begin();
             it != quantMethod->getChannelInformation().end();
             ++it)
        {
          currentLine.push_back(String(intensityMap[int(it->center)]));
        }

        textFile.addLine(ListUtils::concatenate(currentLine, "\t"));
      }
    }

    // write to file
    textFile.store(filename);
  }