FeatureLinkerBase.cpp

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Clemens Groepl, Steffen Sass $
// --------------------------------------------------------------------------
 
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithm.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/ExperimentalDesign.h>
#include <OpenMS/FORMAT/ExperimentalDesignFile.h>
 
#include <OpenMS/KERNEL/ConversionHelper.h>
 
#include <OpenMS/APPLICATIONS/TOPPBase.h>
 
#include <iomanip>     // setw
 
using namespace OpenMS;
using namespace std;
 
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
 
// We do not want this class to show up in the docu:
 
class TOPPFeatureLinkerBase :
  public TOPPBase, 
  public ProgressLogger
{
 
public:
  TOPPFeatureLinkerBase(String name, String description, bool official = true) :
    TOPPBase(name, description, official)
  {
  }
 
protected:
  void registerOptionsAndFlags_() override   // only for "unlabeled" algorithms!
  {
    registerInputFileList_("in", "<files>", ListUtils::create<String>(""), "input files separated by blanks", true);
    setValidFormats_("in", ListUtils::create<String>("featureXML,consensusXML"));
    registerOutputFile_("out", "<file>", "", "Output file", true);
    setValidFormats_("out", ListUtils::create<String>("consensusXML"));
    registerInputFile_("design", "<file>", "", "input file containing the experimental design", false);
    setValidFormats_("design", ListUtils::create<String>("tsv"));
    addEmptyLine_();
    registerFlag_("keep_subelements", "For consensusXML input only: If set, the sub-features of the inputs are transferred to the output.");
  }
 
  ExitCodes common_main_(FeatureGroupingAlgorithm * algorithm,
                         bool labeled = false)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    StringList ins;
    if (labeled)
    {
      ins.push_back(getStringOption_("in"));
    }
    else
    {
      ins = getStringList_("in");
    }
    String out = getStringOption_("out");
    
    //-------------------------------------------------------------
    // check for valid input
    //-------------------------------------------------------------
    // check if all input files have the correct type
    FileTypes::Type file_type = FileHandler::getType(ins[0]);
    for (Size i = 0; i < ins.size(); ++i)
    {
      if (FileHandler::getType(ins[i]) != file_type)
      {
        writeLogError_("Error: All input files must be of the same type!");
        return ILLEGAL_PARAMETERS;
      }
    }
 
    //-------------------------------------------------------------
    // set up algorithm
    //-------------------------------------------------------------
    Param algorithm_param = getParam_().copy("algorithm:", true);
    writeDebug_("Used algorithm parameters", algorithm_param, 3);
    algorithm->setParameters(algorithm_param);
 
    //-------------------------------------------------------------
    // perform grouping
    //-------------------------------------------------------------
    // load input
    ConsensusMap out_map;
    StringList ms_run_locations;
 
    String design_file;
 
    // TODO: support design in labeled feature linker
    if (!labeled)
    {
      design_file = getStringOption_("design");
    }
 
    if (file_type == FileTypes::CONSENSUSXML && !design_file.empty())
    {
      writeLogError_("Error: Using fractionated design with consensusXML als input is not supported!");
      return ILLEGAL_PARAMETERS;
    }
  
    if (file_type == FileTypes::FEATUREXML)
    {
      OPENMS_LOG_INFO << "Linking " << ins.size() << " featureXMLs." << endl;
  
      //-------------------------------------------------------------
      // Extract (optional) fraction identifiers and associate with featureXMLs
      //-------------------------------------------------------------
 
      // determine map of fractions to MS files
      map<unsigned, vector<String>> frac2files;
 
      if (!design_file.empty())
      {
        // parse design file and determine fractions
        ExperimentalDesign ed = ExperimentalDesignFile::load(design_file, false);
 
        // determine if design defines more than one fraction
        frac2files = ed.getFractionToMSFilesMapping();
 
        writeDebug_(String("Grouping ") + String(ed.getNumberOfFractions()) + " fractions.", 3);
 
        // check if all fractions have the same number of MS runs associated
        if (!ed.sameNrOfMSFilesPerFraction())
        {
          writeLogError_("Error: Number of runs must match for every fraction!");
          return ILLEGAL_PARAMETERS;
        }
      }
      else // no design file given
      {
        for (Size i = 0; i != ins.size(); ++i)
        {
          frac2files[1].emplace_back(String("file") + String(i)); // associate each run with fraction 1
        }
      }
 
      vector<FeatureMap > maps(ins.size());
      FileHandler f;
      FeatureFileOptions param = f.getFeatOptions();
 
      // to save memory don't load convex hulls and subordinates
      param.setLoadSubordinates(false);
      param.setLoadConvexHull(false);
      f.setFeatOptions(param);
 
      Size progress = 0;
      setLogType(ProgressLogger::CMD);
      startProgress(0, ins.size(), "reading input");
      for (Size i = 0; i < ins.size(); ++i)
      {
        FeatureMap tmp;
        f.loadFeatures(ins[i], tmp, {FileTypes::FEATUREXML});
 
        StringList ms_runs;
        tmp.getPrimaryMSRunPath(ms_runs);
 
        // associate mzML file with map i in consensusXML
        if (ms_runs.size() > 1 || ms_runs.empty())
        {
          OPENMS_LOG_WARN << "Exactly one MS run should be associated with a FeatureMap. "
            << ms_runs.size() 
            << " provided." << endl;
        }
        else
        {
          out_map.getColumnHeaders()[i].filename = ms_runs.front();
        }
        out_map.getColumnHeaders()[i].size = tmp.size();
        out_map.getColumnHeaders()[i].unique_id = tmp.getUniqueId();
 
        // copy over information on the primary MS run
        ms_run_locations.insert(ms_run_locations.end(), ms_runs.begin(), ms_runs.end());
 
        // to save memory, remove convex hulls, subordinates:
        for (Feature& ft : tmp)
        {
          String adduct;
          String group;
          //exception: addduct information
          if (ft.metaValueExists(Constants::UserParam::DC_CHARGE_ADDUCTS))
          {
            adduct = ft.getMetaValue(Constants::UserParam::DC_CHARGE_ADDUCTS);
          }
          if (ft.metaValueExists(Constants::UserParam::ADDUCT_GROUP))
          {
            group = ft.getMetaValue(Constants::UserParam::ADDUCT_GROUP);
          }
          ft.getSubordinates().clear();
          ft.getConvexHulls().clear();
          ft.clearMetaInfo();
          if (!adduct.empty())
          {
            ft.setMetaValue(Constants::UserParam::DC_CHARGE_ADDUCTS, adduct);
          }
          if (!group.empty())
          {
            ft.setMetaValue("Group", group);
          }
 
        }
 
        maps[i] = tmp;
        maps[i].updateRanges();
 
        setProgress(progress++);
      }
      endProgress();
 
      // exception for "labeled" algorithms: copy file descriptions
      if (labeled)
      {
        out_map.getColumnHeaders()[1] = out_map.getColumnHeaders()[0];
        out_map.getColumnHeaders()[0].label = "light";
        out_map.getColumnHeaders()[1].label = "heavy";
        ms_run_locations.push_back(ms_run_locations[0]);
      }
 
      // invoke feature grouping algorithm
      
      if (frac2files.size() == 1) // group one fraction
      {
        algorithm->group(maps, out_map);
      }
      else // group multiple fractions
      {
        writeDebug_(String("Stored in ") + String(maps.size()) + " maps.", 3);
        for (Size i = 1; i <= frac2files.size(); ++i)
        {
          vector<FeatureMap> fraction_maps;
          // TODO FRACTIONS: here we assume that the order of featureXML is from fraction 1..n
          // we should check if these are shuffled and error / warn          
          for (size_t feature_map_index = 0; feature_map_index != frac2files[i].size(); ++feature_map_index)
          {
            fraction_maps.push_back(maps[feature_map_index]);
          }
          algorithm->group(fraction_maps, out_map);
        }
      }
    }
    else
    {
      //TODO isn't it better to have this option/functionality in the FeatureGroupingAlgorithm class?
      // Otherwise everyone has to remember e.g. to annotate the old map_index etc.
      bool keep_subelements = getFlag_("keep_subelements");
      vector<ConsensusMap> maps(ins.size());
      FileHandler f;
      for (Size i = 0; i < ins.size(); ++i)
      {
        f.loadConsensusFeatures(ins[i], maps[i], {FileTypes::CONSENSUSXML});
        maps[i].updateRanges();
        // copy over information on the primary MS run
        StringList ms_runs;
        maps[i].getPrimaryMSRunPath(ms_runs);
        ms_run_locations.insert(ms_run_locations.end(), ms_runs.begin(), ms_runs.end());
        if (keep_subelements)
        {
          auto saveOldMapIndex =
            [](PeptideIdentification &p)
            {
              if (p.metaValueExists("map_index"))
              {
                p.setMetaValue("old_map_index", p.getMetaValue("map_index"));
              }
              else
              {
                OPENMS_LOG_WARN << "Warning: map_index not found in PeptideID. The tool will not be able to assign a"
                                   "consistent one. Check the settings of previous tools." << std::endl;
              }
            };
          maps[i].applyFunctionOnPeptideIDs(saveOldMapIndex, true);
        }
      }
      // group
      algorithm->group(maps, out_map);
 
      // set file descriptions:
 
      if (!keep_subelements)
      {
        for (Size i = 0; i < ins.size(); ++i)
        {
          out_map.getColumnHeaders()[i].filename = ins[i];
          out_map.getColumnHeaders()[i].size = maps[i].size();
          out_map.getColumnHeaders()[i].unique_id = maps[i].getUniqueId();
        }
      }
      else
      {
        // components of the output map are not the input maps themselves, but
        // the components of the input maps:
        algorithm->transferSubelements(maps, out_map);
      }
    }
 
    // assign unique ids
    out_map.applyMemberFunction(&UniqueIdInterface::setUniqueId);
 
    // annotate output with data processing info
    addDataProcessing_(out_map,
                       getProcessingInfo_(DataProcessing::FEATURE_GROUPING));
 
 
    // sort list of peptide identifications in each consensus feature by map index
    out_map.sortPeptideIdentificationsByMapIndex();
 
    // write output
    FileHandler().storeConsensusFeatures(out, out_map, {FileTypes::CONSENSUSXML});
 
    // some statistics
    map<Size, UInt> num_consfeat_of_size;
    for (const ConsensusFeature& cf : out_map)
    {
      ++num_consfeat_of_size[cf.size()];
    }
 
    OPENMS_LOG_INFO << "Number of consensus features:" << endl;
    for (map<Size, UInt>::reverse_iterator i = num_consfeat_of_size.rbegin();
         i != num_consfeat_of_size.rend(); ++i)
    {
      OPENMS_LOG_INFO << "  of size " << setw(2) << i->first << ": " << setw(6) 
               << i->second << endl;
    }
    OPENMS_LOG_INFO << "  total:      " << setw(6) << out_map.size() << endl;
 
    return EXECUTION_OK;
  }
 
};