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Merge pull request #2946 from grosenberger/feature/percolator_osw
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[FEATURE] OpenSWATH Support for PercolatorAdapter
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@hroest
hroest committed Oct 20, 2017
2 parents b1581ca + ba6e721 commit 91866b9
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91 changes: 91 additions & 0 deletions src/openms/include/OpenMS/FORMAT/OSWFile.h
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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// 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: George Rosenberger $
// $Authors: George Rosenberger $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_OSWFILE_H
#define OPENMS_FORMAT_OSWFILE_H

#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <sqlite3.h>

namespace OpenMS
{
/**
@brief This class serves for reading in and writing OpenSWATH OSW files.
The reader and writer returns data in a format suitable for PercolatorAdapter.
OSW files have a flexible data structure. They contain all peptide query
parameters of TraML/PQP files with the detected and quantified features of
OpenSwathWorkflow (feature, feature_ms1, feature_ms2 & feature_transition).
The OSWFile reader extracts the feature information from the OSW file for
each level (MS1, MS2 & transition) separately and generates Percolator input
files. For each of the three Percolator reports, OSWFile writer adds a table
(score_ms1, score_ms2, score_transition) with the respective confidence metrics.
These tables can be mapped to the corresponding feature tables, are very similar
to PyProphet results and can thus be used interchangeably.
*/
class OPENMS_DLLAPI OSWFile
{
public:
/// Default constructor
OSWFile();

/// Destructor
virtual ~OSWFile();

/**
@brief Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level
as stringstream TXT input for PercolatorAdapter.
*/
void read(const std::string& in_osw, const std::string& osw_level, std::stringstream& pin_output, const double& ipf_max_peakgroup_pep, const double& ipf_max_transition_isotope_overlap, const double& ipf_min_transition_sn);

/**
@brief Updates an OpenSWATH OSW SQLite files with the MS1-, MS2- or transition-level results of Percolator.
*/
void write(const std::string& in_osw, const std::string& osw_level, const std::map< std::string, std::vector<double> >& features);

private:
/**
@brief Helper function for writing OSW SQLite files
*/
static int callback(void * /* NotUsed */, int argc, char **argv, char **azColName);

};

} // namespace OpenMS

#endif // OPENMS_FORMAT_OSWFILE_H
1 change: 1 addition & 0 deletions src/openms/include/OpenMS/FORMAT/sources.cmake
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Expand Up @@ -64,6 +64,7 @@ MzTabFile.h
MzXMLFile.h
OMSSACSVFile.h
OMSSAXMLFile.h
OSWFile.h
ParamXMLFile.h
PTMXMLFile.h
PeakTypeEstimator.h
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271 changes: 271 additions & 0 deletions src/openms/source/FORMAT/OSWFile.cpp
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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// 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: George Rosenberger $
// $Authors: George Rosenberger $
// --------------------------------------------------------------------------

#include <OpenMS/FORMAT/OSWFile.h>

namespace OpenMS
{
using namespace std;

OSWFile::OSWFile()
{
}

OSWFile::~OSWFile()
{
}

void OSWFile::read(const std::string& in_osw, const std::string& osw_level, std::stringstream& pin_output, const double& ipf_max_peakgroup_pep, const double& ipf_max_transition_isotope_overlap, const double& ipf_min_transition_sn) {

sqlite3 *db;
sqlite3_stmt * stmt;
int rc;
std::string select_sql;

// Open database
rc = sqlite3_open(in_osw.c_str(), &db);
if ( rc )
{
fprintf(stderr, "Can't open database: %s\n", sqlite3_errmsg(db));
}

if (osw_level == "ms1") {
select_sql = "SELECT *, RUN_ID || '_' || PRECURSOR.ID AS GROUP_ID FROM FEATURE_MS1 INNER JOIN (SELECT ID, PRECURSOR_ID, RUN_ID FROM FEATURE) AS FEATURE ON FEATURE_ID = FEATURE.ID INNER JOIN (SELECT ID, DECOY FROM PRECURSOR) AS PRECURSOR ON FEATURE.PRECURSOR_ID = PRECURSOR.ID INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID INNER JOIN (SELECT ID, MODIFIED_SEQUENCE FROM PEPTIDE) AS PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID;";
} else if (osw_level == "transition") {
select_sql = "SELECT TRANSITION.DECOY AS DECOY, FEATURE_TRANSITION.*, RUN_ID || '_' || FEATURE_TRANSITION.FEATURE_ID || '_' || PRECURSOR_ID || '_' || TRANSITION_ID AS GROUP_ID, FEATURE_TRANSITION.FEATURE_ID || '_' || FEATURE_TRANSITION.TRANSITION_ID AS FEATURE_ID, 'PEPTIDE' AS MODIFIED_SEQUENCE FROM FEATURE_TRANSITION INNER JOIN (SELECT RUN_ID, ID, PRECURSOR_ID FROM FEATURE) AS FEATURE ON FEATURE_TRANSITION.FEATURE_ID = FEATURE.ID INNER JOIN PRECURSOR ON FEATURE.PRECURSOR_ID = PRECURSOR.ID INNER JOIN SCORE_MS2 ON FEATURE.ID = SCORE_MS2.FEATURE_ID INNER JOIN (SELECT ID, DECOY FROM TRANSITION) AS TRANSITION ON FEATURE_TRANSITION.TRANSITION_ID = TRANSITION.ID WHERE PEP <= " + OpenMS::String(ipf_max_peakgroup_pep) + " AND VAR_ISOTOPE_OVERLAP_SCORE <= " + OpenMS::String(ipf_max_transition_isotope_overlap) + " AND VAR_LOG_SN_SCORE > " + OpenMS::String(ipf_min_transition_sn) + " AND PRECURSOR.DECOY == 0 ORDER BY FEATURE_ID, PRECURSOR_ID, TRANSITION_ID;";
} else {
// Peak group-level query including peptide sequence
select_sql = "SELECT *, RUN_ID || '_' || PRECURSOR.ID AS GROUP_ID FROM FEATURE_MS2 INNER JOIN (SELECT ID, PRECURSOR_ID, RUN_ID FROM FEATURE) AS FEATURE ON FEATURE_ID = FEATURE.ID INNER JOIN (SELECT ID, DECOY FROM PRECURSOR) AS PRECURSOR ON FEATURE.PRECURSOR_ID = PRECURSOR.ID INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID INNER JOIN (SELECT ID, MODIFIED_SEQUENCE FROM PEPTIDE) AS PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID;";
}

// Execute SQL select statement
sqlite3_prepare(db, select_sql.c_str(), -1, &stmt, NULL);
sqlite3_step( stmt );

int cols = sqlite3_column_count(stmt);

// Generate features
int k = 0;
std::vector<std::string> group_id_index;

while (sqlite3_column_type( stmt, 0 ) != SQLITE_NULL)
{
std::string psm_id;
size_t scan_id = 0;
int label = 0;
std::string peptide;
std::map<std::string, double> features;

for (int i = 0; i < cols; i++)
{
if (OpenMS::String(sqlite3_column_name( stmt, i )) == "FEATURE_ID")
{
psm_id = OpenMS::String(reinterpret_cast<const char*>(sqlite3_column_text( stmt, i )));
}
if (OpenMS::String(sqlite3_column_name( stmt, i )) == "GROUP_ID")
{
if (std::find(group_id_index.begin(), group_id_index.end(), OpenMS::String(reinterpret_cast<const char*>(sqlite3_column_text( stmt, i )))) != group_id_index.end())
{
scan_id = std::find(group_id_index.begin(), group_id_index.end(), OpenMS::String(reinterpret_cast<const char*>(sqlite3_column_text( stmt, i )))) - group_id_index.begin();
}
else
{
group_id_index.push_back(OpenMS::String(reinterpret_cast<const char*>(sqlite3_column_text( stmt, i ))));
scan_id = std::find(group_id_index.begin(), group_id_index.end(), OpenMS::String(reinterpret_cast<const char*>(sqlite3_column_text( stmt, i )))) - group_id_index.begin();
}
}
if (OpenMS::String(sqlite3_column_name( stmt, i )) == "DECOY")
{
if (sqlite3_column_int( stmt, i ) == 1)
{
label = -1;
}
else
{
label = 1;
}
}
if (OpenMS::String(sqlite3_column_name( stmt, i )) == "MODIFIED_SEQUENCE")
{
peptide = OpenMS::String(reinterpret_cast<const char*>(sqlite3_column_text( stmt, i )));
}
if (OpenMS::String(sqlite3_column_name( stmt, i )).substr(0,4) == "VAR_")
{
features[OpenMS::String(sqlite3_column_name( stmt, i ))] = sqlite3_column_double( stmt, i );
}
}

// Write output
if (k == 0)
{
pin_output << "PSMId\tLabel\tScanNr";
for (auto const &feat : features)
{
pin_output << "\t" << feat.first;
}
pin_output << "\tPeptide\tProteins\n";
}
pin_output << psm_id << "\t" << label << "\t" << scan_id;
for (auto const &feat : features)
{
pin_output << "\t" << feat.second;
}
pin_output << "\t." << peptide << ".\tProt1" << "\n";

sqlite3_step( stmt );
k++;
}

sqlite3_finalize(stmt);
sqlite3_close(db);

if (k==0)
{
if (osw_level == "transition")
{
throw Exception::Precondition(__FILE__, __LINE__, __FUNCTION__, OpenMS::String("PercolatorAdapter needs to be applied on MS1 & MS2 levels before conducting transition-level scoring."));
}
else
{
throw Exception::FileEmpty(__FILE__, __LINE__, __FUNCTION__, in_osw);
}
}
}

void OSWFile::write(const std::string& in_osw, const std::string& osw_level, const std::map< std::string, std::vector<double> >& features) {
std::string table;
std::string create_sql;

if (osw_level == "ms1") {
table = "SCORE_MS1";
create_sql = "DROP TABLE IF EXISTS " + table + "; " \
"CREATE TABLE " + table + "(" \
"FEATURE_ID INT NOT NULL," \
"SCORE DOUBLE NOT NULL," \
"QVALUE DOUBLE NOT NULL," \
"PEP DOUBLE NOT NULL);";

} else if (osw_level == "transition") {
table = "SCORE_TRANSITION";
create_sql = "DROP TABLE IF EXISTS " + table + "; " \
"CREATE TABLE " + table + "(" \
"FEATURE_ID INT NOT NULL," \
"TRANSITION_ID INT NOT NULL," \
"SCORE DOUBLE NOT NULL," \
"QVALUE DOUBLE NOT NULL," \
"PEP DOUBLE NOT NULL);";

} else {
table = "SCORE_MS2";
create_sql = "DROP TABLE IF EXISTS " + table + "; " \
"CREATE TABLE " + table + "(" \
"FEATURE_ID INT NOT NULL," \
"SCORE DOUBLE NOT NULL," \
"QVALUE DOUBLE NOT NULL," \
"PEP DOUBLE NOT NULL);";
}

std::vector<std::string> insert_sqls;
for (auto const &feat : features)
{
std::stringstream insert_sql;
if (osw_level == "transition") {
std::vector<OpenMS::String> ids;
OpenMS::String(feat.first).split("_", ids);
insert_sql << "INSERT INTO " << table;
insert_sql << " (FEATURE_ID, TRANSITION_ID, SCORE, QVALUE, PEP) VALUES (";
insert_sql << ids[0] << ",";
insert_sql << ids[1] << ",";
insert_sql << feat.second[0] << ",";
insert_sql << feat.second[1] << ",";
insert_sql << feat.second[2] << "); ";
}
else {
insert_sql << "INSERT INTO " << table;
insert_sql << " (FEATURE_ID, SCORE, QVALUE, PEP) VALUES (";
insert_sql << feat.first << ",";
insert_sql << feat.second[0] << ",";
insert_sql << feat.second[1] << ",";
insert_sql << feat.second[2] << "); ";
}

insert_sqls.push_back(insert_sql.str());
}

// Conduct SQLite operations
sqlite3 *db;
char *zErrMsg = 0;
int rc;

// Open database
rc = sqlite3_open(in_osw.c_str(), &db);
if ( rc )
{
fprintf(stderr, "Can't open database: %s\n", sqlite3_errmsg(db));
}

// Execute SQL create statement
rc = sqlite3_exec(db, create_sql.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
}

sqlite3_exec(db, "BEGIN TRANSACTION", NULL, NULL, &zErrMsg);

for (size_t i = 0; i < insert_sqls.size(); i++)
{
rc = sqlite3_exec(db, insert_sqls[i].c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
}
}

sqlite3_exec(db, "END TRANSACTION", NULL, NULL, &zErrMsg);
sqlite3_close(db);
}

int OSWFile::callback(void * /* NotUsed */, int argc, char **argv, char **azColName)
{
int i;
for (i=0; i<argc; i++)
{
printf("%s = %s\n", azColName[i], argv[i] ? argv[i] : "NULL");
}
printf("\n");
return(0);
}

} // namespace OpenMS
1 change: 1 addition & 0 deletions src/openms/source/FORMAT/sources.cmake
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Expand Up @@ -48,6 +48,7 @@ MzTabFile.cpp
MzXMLFile.cpp
OMSSACSVFile.cpp
OMSSAXMLFile.cpp
OSWFile.cpp
ParamXMLFile.cpp
PTMXMLFile.cpp
PeakTypeEstimator.cpp
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Binary file added src/tests/topp/THIRDPARTY/PercolatorAdapter_2.osw
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6 changes: 6 additions & 0 deletions src/tests/topp/THIRDPARTY/third_party_tests.cmake
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Expand Up @@ -132,6 +132,12 @@ if (NOT (${PERCOLATOR_BINARY} STREQUAL "PERCOLATOR_BINARY-NOTFOUND"))
add_test("TOPP_PercolatorAdapter_1" ${TOPP_BIN_PATH}/PercolatorAdapter -test -ini ${DATA_DIR_TOPP}/THIRDPARTY/PercolatorAdapter_1.ini -in ${DATA_DIR_TOPP}/THIRDPARTY/PercolatorAdapter_1.idXML -out PercolatorAdapter_1_out1.tmp -percolator_executable "${PERCOLATOR_BINARY}")
add_test("TOPP_PercolatorAdapter_1_out1" ${DIFF} -in1 PercolatorAdapter_1_out1.tmp -in2 ${DATA_DIR_TOPP}/THIRDPARTY/PercolatorAdapter_1_out.idXML -whitelist "IdentificationRun date" "SearchParameters id=\"SP_0\" db=" "UserParam type=\"stringList\" name=\"spectra_data\" value=")
set_tests_properties("TOPP_PercolatorAdapter_1_out1" PROPERTIES DEPENDS "TOPP_PercolatorAdapter_1")
add_test("TOPP_PercolatorAdapter_2" ${TOPP_BIN_PATH}/PercolatorAdapter -test -osw_level ms1 -in_osw ${DATA_DIR_TOPP}/THIRDPARTY/PercolatorAdapter_2.osw -osw_out PercolatorAdapter_2_out1.osw -percolator_executable "${PERCOLATOR_BINARY}")
add_test("TOPP_PercolatorAdapter_3" ${TOPP_BIN_PATH}/PercolatorAdapter -test -osw_level ms2 -in_osw PercolatorAdapter_2_out1.osw -osw_out PercolatorAdapter_3_out1.osw -percolator_executable "${PERCOLATOR_BINARY}")
set_tests_properties("TOPP_PercolatorAdapter_3" PROPERTIES DEPENDS "TOPP_PercolatorAdapter_2")
add_test("TOPP_PercolatorAdapter_4" ${TOPP_BIN_PATH}/PercolatorAdapter -test -osw_level transition -in_osw PercolatorAdapter_3_out1.osw -osw_out PercolatorAdapter_4_out1.osw -percolator_executable "${PERCOLATOR_BINARY}")
set_tests_properties("TOPP_PercolatorAdapter_4" PROPERTIES DEPENDS "TOPP_PercolatorAdapter_3")
### TOPP_PercolatorAdapter_2-4 do not validate output, but checks whether OSW files can be read and written to.
endif()

#------------------------------------------------------------------------------
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