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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: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/ANALYSIS/ID/IDDecoyProbability.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
using namespace OpenMS;
using namespace std;
/**
@page UTILS_IDDecoyProbability IDDecoyProbability
@brief Util to estimate probability of peptide hits
<CENTER>
<table>
<tr>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. predecessor tools </td>
<td VALIGN="middle" ROWSPAN=3> \f$ \longrightarrow \f$ IDDecoyProbability \f$ \longrightarrow \f$</td>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. successor tools </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_MascotAdapter (or other ID engines) </td>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=2> - </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_PeptideIndexer </td>
</tr>
</table>
</CENTER>
@experimental This util is deprecated and might behave not as expected!
So far an estimation of the false score distribution with a gamma distribution
and the correct score distribution with a gaussian distribution is performed.
The probabilities are calculated using bayes law, similar to PeptideProphet.
This implementation is much simpler than that of PeptideProphet.
<B>The command line parameters of this tool are:</B>
@verbinclude UTILS_IDDecoyProbability.cli
<B>INI file documentation of this tool:</B>
@htmlinclude UTILS_IDDecoyProbability.html
For the parameters of the algorithm section see the algorithms documentation: @n
@ref OpenMS::IDDecoyProbability "decoy_algorithm" @n
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPIDDecoyProbability :
public TOPPBase
{
public:
TOPPIDDecoyProbability() :
TOPPBase("IDDecoyProbability", "Estimates peptide probabilities using a decoy search strategy.\nWARNING: This util is deprecated.", false)
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "Identification input of combined forward decoy search (reindex with PeptideIndexer first)", false);
setValidFormats_("in", StringList::create("idXML"));
registerInputFile_("fwd_in", "<file>", "", "Identification input of forward run", false);
setValidFormats_("fwd_in", StringList::create("idXML"));
registerInputFile_("rev_in", "<file>", "", "Identification input of decoy run", false);
setValidFormats_("rev_in", StringList::create("idXML"));
registerOutputFile_("out", "<file>", "", "Identification output with forward scores converted to probabilities");
setValidFormats_("out", StringList::create("idXML"));
registerSubsection_("decoy_algorithm", "Algorithm parameter subsection");
addEmptyLine_();
}
Param getSubsectionDefaults_(const String & /*section*/) const
{
IDDecoyProbability decoy_prob;
return decoy_prob.getParameters();
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
//input/output files
// either fwd_in and rev_in must be given or just the in which contains results of a search against a concatenated target decoy sequence db
String fwd_in(getStringOption_("fwd_in")), rev_in(getStringOption_("rev_in")), in(getStringOption_("in"));
bool combined(false);
if (fwd_in != "" && rev_in != "")
{
if (in != "")
{
writeLog_("Error, either 'fwd_in' and 'rev_in' must be given or 'in', but not both");
return ILLEGAL_PARAMETERS;
}
}
else
{
if (in != "")
{
combined = true;
}
else
{
writeLog_("Error, at least 'fwd_in' and 'rev_in' or 'in' must be given");
return ILLEGAL_PARAMETERS;
}
}
String out(getStringOption_("out"));
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
IDDecoyProbability decoy_prob;
Param decoy_param = getParam_().copy("decoy_algorithm:", true);
decoy_prob.setParameters(decoy_param);
if (!combined)
{
vector<PeptideIdentification> fwd_pep, rev_pep, out_pep;
vector<ProteinIdentification> fwd_prot, rev_prot;
String document_id;
IdXMLFile().load(fwd_in, fwd_prot, fwd_pep, document_id);
IdXMLFile().load(rev_in, rev_prot, rev_pep, document_id);
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
writeDebug_("Starting calculations", 1);
decoy_prob.apply(out_pep, fwd_pep, rev_pep);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
IdXMLFile().store(out, fwd_prot, out_pep);
}
else
{
vector<ProteinIdentification> prot_ids;
vector<PeptideIdentification> pep_ids;
String document_id;
IdXMLFile().load(in, prot_ids, pep_ids, document_id);
decoy_prob.apply(pep_ids);
IdXMLFile().store(out, prot_ids, pep_ids);
}
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPIDDecoyProbability tool;
return tool.main(argc, argv);
}
/// @endcond
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