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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <fstream>
using namespace OpenMS;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page UTILS_OpenSwathRewriteToFeatureXML OpenSwathRewriteToFeatureXML
@brief Combines featureXML and mProphet tsv to FDR filtered featureXML.
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPOpenSwathRewriteToFeatureXML
: public TOPPBase,
public ProgressLogger
{
public:
TOPPOpenSwathRewriteToFeatureXML()
: TOPPBase("OpenSwathRewriteToFeatureXML","Combines featureXML and mProphet tsv to FDR filtered featureXML.")
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("csv","<file>","","mProphet tsv output file: \"all_peakgroups.xls\"", false);
setValidFormats_("csv", StringList::create("csv"));
registerInputFile_("featureXML","<file>","","input featureXML file");
setValidFormats_("featureXML", StringList::create("featureXML"));
registerOutputFile_("out","<file>","","output featureXML file");
setValidFormats_("out", StringList::create("featureXML"));
registerDoubleOption_("FDR_cutoff", "<double>", -1, "FDR cutoff (e.g. to remove all features with a an m_score above 0.05 use 0.05 here)", false);
}
void applyFDRcutoff(FeatureMap<Feature> & feature_map, double cutoff, String fdr_name)
{
FeatureMap<Feature> out_feature_map = feature_map;
out_feature_map.clear(false);
for (Size i = 0; i < feature_map.size(); i++)
{
if ((DoubleReal)feature_map[i].getMetaValue(fdr_name) < cutoff)
{
out_feature_map.push_back(feature_map[i]);
}
}
feature_map = out_feature_map;
}
void processInput(const char * filename, FeatureMap<Feature> & feature_map)
{
FeatureMap<Feature> out_feature_map = feature_map;
std::map<String, int> added_already;
out_feature_map.clear(false);
std::map<String, Feature*> feature_map_ref;
//for (FeatureMap<Feature>::iterator feature = feature_map.begin(); feature != feature_map.end(); feature++)
for (Size i = 0; i < feature_map.size(); i++)
{
feature_map_ref[feature_map[i].getUniqueId()] = &feature_map[i];
}
std::ifstream data(filename);
std::string line;
// Read header
std::getline(data, line);
// std::map<int, String> header_dict; // not used
std::map<String, int> header_dict_inv;
{
std::stringstream lineStream(line);
std::string cell;
int cnt = 0;
while (std::getline(lineStream,cell,'\t'))
{
//header_dict[cnt] = cell;
header_dict_inv[cell] = cnt;
cnt++;
}
}
if (header_dict_inv.find("id") == header_dict_inv.end() ||
header_dict_inv.find("m_score") == header_dict_inv.end() ||
header_dict_inv.find("d_score") == header_dict_inv.end() )
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Error: The tsv file is expected to have at least the following headers: id, m_score, d_score. " );
}
// Read file
std::vector<std::string> current_row;
std::string cell;
int line_nr = 0;
DoubleReal m_score, d_score;
while (std::getline(data, line))
{
line_nr++;
current_row.clear();
std::stringstream lineStream(line);
while (std::getline(lineStream,cell,'\t'))
{
current_row.push_back(cell);
}
String id = current_row[header_dict_inv["id"]];
id = id.substitute("f_", "");
try
{
m_score = ((String)current_row[header_dict_inv["m_score"]]).toDouble();
}
catch (char* /*str*/)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Error: Could not convert String" + ((String)current_row[header_dict_inv["m_score"]]) + " on line " + String(line_nr));
}
try
{
d_score = ((String)current_row[header_dict_inv["d_score"]]).toDouble();
}
catch (char* /*str*/)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Error: Could not convert String" + ((String)current_row[header_dict_inv["d_score"]]) + " on line " + String(line_nr));
}
if (feature_map_ref.find(id) != feature_map_ref.end() )
{
Feature* feature = feature_map_ref.find(id)->second;
feature->setMetaValue("m_score", m_score);
feature->setMetaValue("d_score", d_score);
// we are not allowed to have duplicate unique ids
if (added_already.find(id) != added_already.end())
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Error: Duplicate id found in CSV file: " + id );
}
out_feature_map.push_back(*feature);
}
}
feature_map = out_feature_map;
}
ExitCodes main_(int , const char**)
{
String feature_file = getStringOption_("featureXML");
String csv = getStringOption_("csv");
String out = getStringOption_("out");
DoubleReal fdr_cutoff = getDoubleOption_("FDR_cutoff");
FeatureMap<Feature> feature_map;
FeatureXMLFile().load(feature_file, feature_map);
if (csv.size() > 0)
{
processInput(csv.c_str(), feature_map);
}
if (fdr_cutoff >= 0)
{
applyFDRcutoff(feature_map, fdr_cutoff, "m_score");
}
feature_map.applyMemberFunction(&UniqueIdInterface::ensureUniqueId);
FeatureXMLFile().store(out, feature_map);
return EXECUTION_OK;
}
};
int main( int argc, const char** argv )
{
TOPPOpenSwathRewriteToFeatureXML tool;
int code = tool.main(argc,argv);
return code;
}
/// @endcond
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