// public methods
void TransitionPQPReader::convertTargetedExperimentToPQP(const char* filename, OpenMS::TargetedExperiment& targeted_exp)
{
if (targeted_exp.containsInvalidReferences())
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Your input file contains invalid references, cannot process file.");
}
writePQPOutput_(filename, targeted_exp);
}
void ChromatogramExtractor::populate_PeptideRTMap(OpenMS::TargetedExperiment& transition_exp, double rt_extraction_window)
{
// Store the peptide retention times in an intermediate map
PeptideRTMap_.clear();
for (Size i = 0; i < transition_exp.getPeptides().size(); i++)
{
const TargetedExperiment::Peptide& pep = transition_exp.getPeptides()[i];
if (pep.rts.empty() || pep.rts[0].getCVTerms()["MS:1000896"].empty())
{
// we dont have retention times -> this is only a problem if we actually
// wanted to use the RT limit feature.
if (rt_extraction_window >= 0)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Error: Peptide " + pep.id + " does not have normalized retention times (term 1000896) which are necessary to perform an RT-limited extraction");
}
continue;
}
PeptideRTMap_[pep.id] = pep.rts[0].getCVTerms()["MS:1000896"][0].getValue().toString().toDouble();
}
}
void OpenSwathHelper::selectSwathTransitions(const OpenMS::TargetedExperiment& targeted_exp,
OpenMS::TargetedExperiment& transition_exp_used, double min_upper_edge_dist,
double lower, double upper)
{
transition_exp_used.setPeptides(targeted_exp.getPeptides());
transition_exp_used.setProteins(targeted_exp.getProteins());
for (Size i = 0; i < targeted_exp.getTransitions().size(); i++)
{
ReactionMonitoringTransition tr = targeted_exp.getTransitions()[i];
if (lower < tr.getPrecursorMZ() && tr.getPrecursorMZ() < upper &&
std::fabs(upper - tr.getPrecursorMZ()) >= min_upper_edge_dist)
{
transition_exp_used.addTransition(tr);
}
}
}
void OpenSwathDataAccessHelper::convertTargetedExp(const OpenMS::TargetedExperiment & transition_exp_, OpenSwath::LightTargetedExperiment & transition_exp)
{
//copy proteins
for (Size i = 0; i < transition_exp_.getProteins().size(); i++)
{
OpenSwath::LightProtein p;
p.id = transition_exp_.getProteins()[i].id;
transition_exp.proteins.push_back(p);
}
//copy peptides
for (Size i = 0; i < transition_exp_.getPeptides().size(); i++)
{
OpenSwath::LightPeptide p;
OpenSwathDataAccessHelper::convertTargetedPeptide(transition_exp_.getPeptides()[i], p);
transition_exp.peptides.push_back(p);
}
//mapping of transitions
for (Size i = 0; i < transition_exp_.getTransitions().size(); i++)
{
OpenSwath::LightTransition t;
t.transition_name = transition_exp_.getTransitions()[i].getNativeID();
t.product_mz = transition_exp_.getTransitions()[i].getProductMZ();
t.precursor_mz = transition_exp_.getTransitions()[i].getPrecursorMZ();
t.library_intensity = transition_exp_.getTransitions()[i].getLibraryIntensity();
t.peptide_ref = transition_exp_.getTransitions()[i].getPeptideRef();
t.charge = transition_exp_.getTransitions()[i].getProduct().getChargeState();
t.decoy = false;
// legacy
#if 1
if (transition_exp_.getTransitions()[i].getCVTerms().has("decoy") &&
transition_exp_.getTransitions()[i].getCVTerms()["decoy"][0].getValue().toString() == "1" )
{
t.decoy = true;
}
else if (transition_exp_.getTransitions()[i].getCVTerms().has("MS:1002007")) // target SRM transition
{
t.decoy = false;
}
else if (transition_exp_.getTransitions()[i].getCVTerms().has("MS:1002008")) // decoy SRM transition
{
t.decoy = true;
}
else if (transition_exp_.getTransitions()[i].getCVTerms().has("MS:1002007") &&
transition_exp_.getTransitions()[i].getCVTerms().has("MS:1002008")) // both == illegal
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Transition " + t.transition_name + " cannot be target and decoy at the same time.");
}
else
#endif
if (transition_exp_.getTransitions()[i].getDecoyTransitionType() == ReactionMonitoringTransition::UNKNOWN ||
transition_exp_.getTransitions()[i].getDecoyTransitionType() == ReactionMonitoringTransition::TARGET)
{
// assume its target
t.decoy = false;
}
else if (transition_exp_.getTransitions()[i].getDecoyTransitionType() == ReactionMonitoringTransition::DECOY)
{
t.decoy = true;
}
transition_exp.transitions.push_back(t);
}
}
void MRMDecoy::generateDecoys(OpenMS::TargetedExperiment& exp, OpenMS::TargetedExperiment& dec,
String method, String decoy_tag, double identity_threshold, int max_attempts,
double mz_threshold, double mz_shift, bool exclude_similar,
double similarity_threshold, bool remove_CNterminal_mods, double precursor_mass_shift,
std::vector<String> fragment_types, std::vector<size_t> fragment_charges,
bool enable_specific_losses, bool enable_unspecific_losses, bool remove_unannotated,
int round_decPow)
{
MRMIonSeries mrmis;
MRMDecoy::PeptideVectorType peptides, decoy_peptides;
MRMDecoy::ProteinVectorType proteins, decoy_proteins;
MRMDecoy::TransitionVectorType decoy_transitions;
for (Size i = 0; i < exp.getProteins().size(); i++)
{
OpenMS::TargetedExperiment::Protein protein = exp.getProteins()[i];
protein.id = decoy_tag + protein.id;
proteins.push_back(protein);
}
std::vector<String> exclusion_peptides;
// Go through all peptides and apply the decoy method to the sequence
// (pseudo-reverse, reverse or shuffle). Then set the peptides and proteins of the decoy
// experiment.
for (Size pep_idx = 0; pep_idx < exp.getPeptides().size(); ++pep_idx)
{
OpenMS::TargetedExperiment::Peptide peptide = exp.getPeptides()[pep_idx];
// continue if the peptide has C/N terminal modifications and we should exclude them
if (remove_CNterminal_mods && MRMDecoy::has_CNterminal_mods(peptide)) {continue; }
peptide.id = decoy_tag + peptide.id;
OpenMS::String original_sequence = peptide.sequence;
if (!peptide.getPeptideGroupLabel().empty())
{
peptide.setPeptideGroupLabel(decoy_tag + peptide.getPeptideGroupLabel());
}
if (method == "pseudo-reverse")
{
peptide = MRMDecoy::pseudoreversePeptide(peptide);
}
else if (method == "reverse")
{
peptide = MRMDecoy::reversePeptide(peptide);
}
else if (method == "shuffle")
{
peptide = MRMDecoy::shufflePeptide(peptide, identity_threshold, -1, max_attempts);
}
for (Size prot_idx = 0; prot_idx < peptide.protein_refs.size(); ++prot_idx)
{
peptide.protein_refs[prot_idx] = decoy_tag + peptide.protein_refs[prot_idx];
}
if (MRMDecoy::AASequenceIdentity(original_sequence, peptide.sequence) > identity_threshold)
{
if (!exclude_similar)
{
std::cout << "Target sequence: " << original_sequence << " Decoy sequence: " << peptide.sequence << " Sequence identity: " << MRMDecoy::AASequenceIdentity(original_sequence, peptide.sequence) << " Identity threshold: " << identity_threshold << std::endl;
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "AA Sequences are too similar. Either decrease identity_threshold and increase max_attempts for the shuffle method or set flag exclude_similar.");
}
else
{
exclusion_peptides.push_back(peptide.id);
}
}
peptides.push_back(peptide);
}
dec.setPeptides(peptides); // temporary set peptides, overwrite later again!
// hash of the peptide reference containing all transitions
MRMDecoy::PeptideTransitionMapType peptide_trans_map;
for (Size i = 0; i < exp.getTransitions().size(); i++)
{
peptide_trans_map[exp.getTransitions()[i].getPeptideRef()].push_back(&exp.getTransitions()[i]);
}
Size progress = 0;
startProgress(0, exp.getTransitions().size(), "Creating decoys");
for (MRMDecoy::PeptideTransitionMapType::iterator pep_it = peptide_trans_map.begin();
pep_it != peptide_trans_map.end(); ++pep_it)
{
String peptide_ref = pep_it->first;
String decoy_peptide_ref = decoy_tag + pep_it->first; // see above, the decoy peptide id is computed deterministically from the target id
const TargetedExperiment::Peptide target_peptide = exp.getPeptideByRef(peptide_ref);
// continue if the peptide has C/N terminal modifications and we should exclude them
if (remove_CNterminal_mods && MRMDecoy::has_CNterminal_mods(target_peptide)) {continue;}
const TargetedExperiment::Peptide decoy_peptide = dec.getPeptideByRef(decoy_peptide_ref);
OpenMS::AASequence target_peptide_sequence = TargetedExperimentHelper::getAASequence(target_peptide);
OpenMS::AASequence decoy_peptide_sequence = TargetedExperimentHelper::getAASequence(decoy_peptide);
int decoy_charge = 1;
int target_charge = 1;
if (decoy_peptide.hasCharge()) {decoy_charge = decoy_peptide.getChargeState();}
if (target_peptide.hasCharge()) {target_charge = target_peptide.getChargeState();}
MRMIonSeries::IonSeries decoy_ionseries = mrmis.getIonSeries(decoy_peptide_sequence, decoy_charge, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, round_decPow);
MRMIonSeries::IonSeries target_ionseries = mrmis.getIonSeries(target_peptide_sequence, target_charge, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, round_decPow);
for (Size i = 0; i < pep_it->second.size(); i++)
{
setProgress(++progress);
const ReactionMonitoringTransition tr = *(pep_it->second[i]);
if (!tr.isDetectingTransition() || tr.getDecoyTransitionType() == ReactionMonitoringTransition::DECOY)
{
continue;
}
ReactionMonitoringTransition decoy_tr = tr; // copy the target transition
decoy_tr.setNativeID(decoy_tag + tr.getNativeID());
decoy_tr.setDecoyTransitionType(ReactionMonitoringTransition::DECOY);
decoy_tr.setPrecursorMZ(tr.getPrecursorMZ() + precursor_mass_shift); // fix for TOPPView: Duplicate precursor MZ is not displayed.
// determine the current annotation for the target ion and then select
// the appropriate decoy ion for this target transition
std::pair<String, double> targetion = mrmis.annotateIon(target_ionseries, tr.getProductMZ(), mz_threshold);
std::pair<String, double> decoyion = mrmis.getIon(decoy_ionseries, targetion.first);
if (method == "shift")
{
decoy_tr.setProductMZ(decoyion.second + mz_shift);
}
else
{
decoy_tr.setProductMZ(decoyion.second);
}
decoy_tr.setPeptideRef(decoy_tag + tr.getPeptideRef());
if (decoyion.second > 0)
{
if (similarity_threshold >= 0)
{
if (std::fabs(tr.getProductMZ() - decoy_tr.getProductMZ()) < similarity_threshold)
{
if (!exclude_similar)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Fragment ions are too similar. Either decrease similarity_threshold or set flag exclude_similar.");
}
else
{
exclusion_peptides.push_back(decoy_tr.getPeptideRef());
}
}
}
decoy_transitions.push_back(decoy_tr);
}
else
{
if (remove_unannotated)
{
exclusion_peptides.push_back(decoy_tr.getPeptideRef());
}
else
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Decoy fragment ion for target fragment ion " + String(targetion.first) + " of peptide " + target_peptide_sequence.toString() + " with precursor charge " + String(target_peptide.getChargeState()) + " could not be mapped. Please check whether it is a valid ion and enable losses or removal of terminal modifications if necessary. Skipping of unannotated target assays is available as last resort.");
}
}
} // end loop over transitions
} // end loop over peptides
endProgress();
MRMDecoy::TransitionVectorType filtered_decoy_transitions;
for (MRMDecoy::TransitionVectorType::iterator tr_it = decoy_transitions.begin(); tr_it != decoy_transitions.end(); ++tr_it)
{
if (std::find(exclusion_peptides.begin(), exclusion_peptides.end(), tr_it->getPeptideRef()) == exclusion_peptides.end())
{
filtered_decoy_transitions.push_back(*tr_it);
}
}
dec.setTransitions(filtered_decoy_transitions);
std::vector<String> protein_ids;
for (Size i = 0; i < peptides.size(); ++i)
{
TargetedExperiment::Peptide peptide = peptides[i];
// Check if peptide has any transitions left
if (std::find(exclusion_peptides.begin(), exclusion_peptides.end(), peptide.id) == exclusion_peptides.end())
{
decoy_peptides.push_back(peptide);
for (Size j = 0; j < peptide.protein_refs.size(); ++j)
{
protein_ids.push_back(peptide.protein_refs[j]);
}
}
else
{
LOG_DEBUG << "[peptide] Skipping " << peptide.id << std::endl;
}
}
for (Size i = 0; i < proteins.size(); ++i)
{
OpenMS::TargetedExperiment::Protein protein = proteins[i];
// Check if protein has any peptides left
if (find(protein_ids.begin(), protein_ids.end(), protein.id) != protein_ids.end())
{
decoy_proteins.push_back(protein);
}
else
{
LOG_DEBUG << "[protein] Skipping " << protein.id << std::endl;
}
}
dec.setPeptides(decoy_peptides);
dec.setProteins(decoy_proteins);
}
void ChromatogramExtractor::prepare_coordinates(std::vector< OpenSwath::ChromatogramPtr > & output_chromatograms,
std::vector< ExtractionCoordinates > & coordinates,
OpenMS::TargetedExperiment & transition_exp_used,
bool enforce_presence_rt,
const bool ms1) const
{
// hash of the peptide reference containing all transitions
typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType;
PeptideTransitionMapType peptide_trans_map;
for (Size i = 0; i < transition_exp_used.getTransitions().size(); i++)
{
peptide_trans_map[transition_exp_used.getTransitions()[i].getPeptideRef()].push_back(&transition_exp_used.getTransitions()[i]);
}
// Determine iteration size (nr peptides or nr transitions)
Size itersize;
if (ms1) {itersize = transition_exp_used.getPeptides().size();}
else {itersize = transition_exp_used.getTransitions().size();}
for (Size i = 0; i < itersize; i++)
{
OpenSwath::ChromatogramPtr s(new OpenSwath::Chromatogram);
output_chromatograms.push_back(s);
ChromatogramExtractor::ExtractionCoordinates coord;
TargetedExperiment::Peptide pep;
OpenMS::ReactionMonitoringTransition transition;
if (ms1)
{
pep = transition_exp_used.getPeptides()[i];
transition = (*peptide_trans_map[pep.id][0]);
coord.mz = transition.getPrecursorMZ();
coord.id = pep.id;
}
else
{
transition = transition_exp_used.getTransitions()[i];
pep = transition_exp_used.getPeptideByRef(transition.getPeptideRef());
coord.mz = transition.getProductMZ();
coord.id = transition.getNativeID();
}
if (pep.rts.empty() || pep.rts[0].getCVTerms()["MS:1000896"].empty())
{
// we dont have retention times -> this is only a problem if we actually
// wanted to use the RT limit feature.
if (enforce_presence_rt)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Error: Peptide " + pep.id + " does not have normalized retention times (term 1000896) which are necessary to perform an RT-limited extraction");
}
coord.rt = -1;
}
else
{
coord.rt = pep.rts[0].getCVTerms()["MS:1000896"][0].getValue().toString().toDouble();
// coord.rt = trafo.apply(coord.rt); // apply RT transformation if necessary
}
coordinates.push_back(coord);
}
// sort result
std::sort(coordinates.begin(), coordinates.end(), ChromatogramExtractor::ExtractionCoordinates::SortExtractionCoordinatesByMZ);
}
void ChromatogramExtractor::return_chromatogram(std::vector< OpenSwath::ChromatogramPtr > & chromatograms,
std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
OpenMS::TargetedExperiment & transition_exp_used, SpectrumSettings settings,
std::vector<OpenMS::MSChromatogram<> > & output_chromatograms, bool ms1) const
{
typedef std::map<String, const ReactionMonitoringTransition* > TransitionMapType;
TransitionMapType trans_map;
for (Size i = 0; i < transition_exp_used.getTransitions().size(); i++)
{
trans_map[transition_exp_used.getTransitions()[i].getNativeID()] = &transition_exp_used.getTransitions()[i];
}
for (Size i = 0; i < chromatograms.size(); i++)
{
const OpenSwath::ChromatogramPtr & chromptr = chromatograms[i];
const ChromatogramExtractor::ExtractionCoordinates & coord = coordinates[i];
TargetedExperiment::Peptide pep;
OpenMS::ReactionMonitoringTransition transition;
OpenMS::MSChromatogram<> chrom;
// copy data
OpenSwathDataAccessHelper::convertToOpenMSChromatogram(chrom, chromptr);
chrom.setNativeID(coord.id);
// Create precursor and set
// 1) the target m/z
// 2) the isolation window (upper/lower)
// 3) the peptide sequence
Precursor prec;
if (ms1)
{
pep = transition_exp_used.getPeptideByRef(coord.id);
prec.setMZ(coord.mz);
chrom.setChromatogramType(ChromatogramSettings::BASEPEAK_CHROMATOGRAM);
}
else
{
transition = (*trans_map[coord.id]);
pep = transition_exp_used.getPeptideByRef(transition.getPeptideRef());
prec.setMZ(transition.getPrecursorMZ());
if (settings.getPrecursors().size() > 0)
{
prec.setIsolationWindowLowerOffset(settings.getPrecursors()[0].getIsolationWindowLowerOffset());
prec.setIsolationWindowUpperOffset(settings.getPrecursors()[0].getIsolationWindowUpperOffset());
}
// Create product and set its m/z
Product prod;
prod.setMZ(transition.getProductMZ());
chrom.setProduct(prod);
chrom.setChromatogramType(ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM);
}
prec.setMetaValue("peptide_sequence", pep.sequence);
chrom.setPrecursor(prec);
// Set the rest of the meta-data
chrom.setInstrumentSettings(settings.getInstrumentSettings());
chrom.setAcquisitionInfo(settings.getAcquisitionInfo());
chrom.setSourceFile(settings.getSourceFile());
for (Size i = 0; i < settings.getDataProcessing().size(); ++i)
{
DataProcessing dp = settings.getDataProcessing()[i];
dp.setMetaValue("performed_on_spectra", "true");
chrom.getDataProcessing().push_back(dp);
}
output_chromatograms.push_back(chrom);
}
}
void TransitionPQPReader::writePQPOutput_(const char* filename, OpenMS::TargetedExperiment& targeted_exp)
{
sqlite3 *db;
char *zErrMsg = 0;
int rc;
// delete file if present
remove(filename);
// Open database
rc = sqlite3_open(filename, &db);
if ( rc )
{
fprintf(stderr, "Can't open database: %s\n", sqlite3_errmsg(db));
}
// Create SQL structure
const char* create_sql =
// protein table
// OpenSWATH proteomics workflows
"CREATE TABLE PROTEIN(" \
"ID INT PRIMARY KEY NOT NULL," \
"PROTEIN_ACCESSION TEXT NOT NULL," \
"DECOY INT NULL);" \
// peptide_protein_mapping table
// OpenSWATH proteomics workflows
"CREATE TABLE PEPTIDE_PROTEIN_MAPPING(" \
"PEPTIDE_ID INT NOT NULL," \
"PROTEIN_ID INT NOT NULL);" \
// peptide table
// OpenSWATH proteomics workflows
"CREATE TABLE PEPTIDE(" \
"ID INT PRIMARY KEY NOT NULL," \
"UNMODIFIED_SEQUENCE TEXT NOT NULL," \
"MODIFIED_SEQUENCE TEXT NOT NULL," \
"DECOY INT NOT NULL);" \
// precursor_peptide_mapping table
// OpenSWATH proteomics workflows
"CREATE TABLE PRECURSOR_PEPTIDE_MAPPING(" \
"PRECURSOR_ID INT NOT NULL," \
"PEPTIDE_ID INT NOT NULL);" \
// compound table
// OpenSWATH metabolomics workflows
"CREATE TABLE COMPOUND(" \
"ID INT PRIMARY KEY NOT NULL," \
"COMPOUND_NAME TEXT NOT NULL," \
"SUM_FORMULA TEXT NOT NULL," \
"SMILES TEXT NOT NULL," \
"DECOY INT NOT NULL);" \
// precursor_compound_mapping table
// OpenSWATH metabolomics workflows
"CREATE TABLE PRECURSOR_COMPOUND_MAPPING(" \
"PRECURSOR_ID INT NOT NULL," \
"COMPOUND_ID INT NOT NULL);" \
// precursor table
"CREATE TABLE PRECURSOR(" \
"ID INT PRIMARY KEY NOT NULL," \
"TRAML_ID TEXT NULL," \
"GROUP_LABEL TEXT NULL," \
"PRECURSOR_MZ REAL NOT NULL," \
"CHARGE INT NULL," \
"LIBRARY_INTENSITY REAL NULL," \
"LIBRARY_RT REAL NULL," \
"DECOY INT NOT NULL);" \
// transition_precursor_mapping table
"CREATE TABLE TRANSITION_PRECURSOR_MAPPING(" \
"TRANSITION_ID INT NOT NULL," \
"PRECURSOR_ID INT NOT NULL);" \
// transition_peptide_mapping table
// IPF proteomics workflows
"CREATE TABLE TRANSITION_PEPTIDE_MAPPING(" \
"TRANSITION_ID INT NOT NULL," \
"PEPTIDE_ID INT NOT NULL);" \
// transition table
"CREATE TABLE TRANSITION(" \
"ID INT PRIMARY KEY NOT NULL," \
"TRAML_ID TEXT NULL," \
"PRODUCT_MZ REAL NOT NULL," \
"CHARGE INT NULL," \
"TYPE CHAR(1) NULL," \
"ORDINAL INT NULL," \
"DETECTING INT NOT NULL," \
"IDENTIFYING INT NOT NULL," \
"QUANTIFYING INT NOT NULL," \
"LIBRARY_INTENSITY REAL NULL," \
"DECOY INT NOT NULL);";
// Execute SQL create statement
rc = sqlite3_exec(db, create_sql, callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Prepare insert statements
// Index maps
std::vector<std::string> group_set, peptide_set, compound_set, protein_set;
std::map<int,double> precursor_mz_map;
std::map<int,bool> precursor_decoy_map;
std::stringstream insert_transition_sql, insert_transition_peptide_mapping_sql, insert_transition_precursor_mapping_sql;
insert_transition_sql.precision(11);
// OpenSWATH: Loop through TargetedExperiment to generate index maps for peptides
Size progress = 0;
startProgress(0, targeted_exp.getPeptides().size(), "Convert peptides");
for (Size i = 0; i < targeted_exp.getPeptides().size(); i++)
{
setProgress(progress++);
OpenMS::TargetedExperiment::Peptide peptide = targeted_exp.getPeptides()[i];
std::string peptide_sequence = TargetedExperimentHelper::getAASequence(peptide).toString();
peptide_set.push_back(peptide_sequence);
group_set.push_back(peptide.id);
}
endProgress();
// OpenSWATH: Loop through TargetedExperiment to generate index maps for compounds
progress = 0;
startProgress(0, targeted_exp.getCompounds().size(), "Convert compounds");
for (Size i = 0; i < targeted_exp.getCompounds().size(); i++)
{
setProgress(progress++);
OpenMS::TargetedExperiment::Compound compound = targeted_exp.getCompounds()[i];
compound_set.push_back(compound.id);
group_set.push_back(compound.id);
}
endProgress();
// OpenSWATH: Group set must be unique
boost::erase(group_set, boost::unique<boost::return_found_end>(boost::sort(group_set)));
// IPF: Loop through all transitions and generate peptidoform data structures
progress = 0;
std::vector<TransitionPQPReader::TSVTransition > transitions;
startProgress(0, targeted_exp.getTransitions().size(), "Convert peptidoforms");
for (Size i = 0; i < targeted_exp.getTransitions().size(); i++)
{
setProgress(progress++);
TransitionPQPReader::TSVTransition transition = convertTransition_(&targeted_exp.getTransitions()[i], targeted_exp);
transitions.push_back(transition);
std::copy( transition.peptidoforms.begin(), transition.peptidoforms.end(), std::inserter( peptide_set, peptide_set.end() ) );
int group_set_index = std::distance(group_set.begin(),std::find(group_set.begin(), group_set.end(), transition.group_id));
if (precursor_mz_map.find(group_set_index) == precursor_mz_map.end())
{
precursor_mz_map[group_set_index] = transition.precursor;
}
if (precursor_decoy_map.find(group_set_index) == precursor_decoy_map.end())
{
if (transition.detecting_transition == 1)
{
precursor_decoy_map[group_set_index] = transition.decoy;
}
}
}
endProgress();
// OpenSWATH: Peptide and compound sets must be unique
boost::erase(peptide_set, boost::unique<boost::return_found_end>(boost::sort(peptide_set)));
boost::erase(compound_set, boost::unique<boost::return_found_end>(boost::sort(compound_set)));
// OpenSWATH: Prepare transition inserts
progress = 0;
startProgress(0, transitions.size(), String("Prepare ") + transitions.size() + " transitions and mapping");
for (Size i = 0; i < transitions.size(); i++)
{
setProgress(progress++);
TransitionPQPReader::TSVTransition transition = transitions[i];
// IPF: Generate transition-peptide mapping tables (one identification transition can map to multiple peptidoforms)
for (Size j = 0; j < transition.peptidoforms.size(); j++)
{
insert_transition_peptide_mapping_sql << "INSERT INTO TRANSITION_PEPTIDE_MAPPING (TRANSITION_ID, PEPTIDE_ID) VALUES (" << i << "," << std::distance(peptide_set.begin(),std::find(peptide_set.begin(), peptide_set.end(), transition.peptidoforms[j])) << "); ";
}
// OpenSWATH: Associate transitions with their precursors
insert_transition_precursor_mapping_sql << "INSERT INTO TRANSITION_PRECURSOR_MAPPING (TRANSITION_ID, PRECURSOR_ID) VALUES (" << i << "," << std::distance(group_set.begin(), std::find(group_set.begin(), group_set.end(),transition.group_id)) << "); ";
std::string transition_charge = "NULL"; // workaround for compounds with missing charge
if (transition.fragment_charge != "NA")
{
transition_charge = transition.fragment_charge;
}
// OpenSWATH: Insert transition data
insert_transition_sql << "INSERT INTO TRANSITION (ID, TRAML_ID, PRODUCT_MZ, CHARGE, TYPE, ORDINAL, DETECTING, IDENTIFYING, QUANTIFYING, LIBRARY_INTENSITY, DECOY) VALUES (" << i << ",'" << transition.transition_name << "'," << transition.product << "," << transition_charge << ",'" << transition.fragment_type<< "'," << transition.fragment_nr << "," << transition.detecting_transition << "," << transition.identifying_transition << "," << transition.quantifying_transition << "," << transition.library_intensity << "," << transition.decoy << "); ";
}
endProgress();
// OpenSWATH: Prepare protein inserts
progress = 0;
startProgress(0, targeted_exp.getProteins().size(), "Prepare protein mapping");
for (Size i = 0; i < targeted_exp.getProteins().size(); i++)
{
setProgress(progress++);
OpenMS::TargetedExperiment::Protein protein = targeted_exp.getProteins()[i];
protein_set.push_back(protein.id);
}
endProgress();
boost::erase(protein_set, boost::unique<boost::return_found_end>(boost::sort(protein_set)));
std::stringstream insert_precursor_sql, insert_precursor_peptide_mapping, insert_precursor_compound_mapping;
insert_precursor_sql.precision(11);
std::vector<std::pair<int, int> > peptide_protein_map;
// OpenSWATH: Prepare peptide precursor inserts
progress = 0;
startProgress(0, targeted_exp.getPeptides().size(), "Prepare peptide precursors and mapping");
for (Size i = 0; i < targeted_exp.getPeptides().size(); i++)
{
setProgress(progress++);
OpenMS::TargetedExperiment::Peptide peptide = targeted_exp.getPeptides()[i];
std::string peptide_sequence = TargetedExperimentHelper::getAASequence(peptide).toString();
int group_set_index = std::distance(group_set.begin(),std::find(group_set.begin(), group_set.end(), peptide.id));
int peptide_set_index = std::distance(peptide_set.begin(), std::find(peptide_set.begin(), peptide_set.end(), peptide_sequence));
for (std::vector<String>::iterator it = peptide.protein_refs.begin(); it != peptide.protein_refs.end(); ++it)
{
int protein_set_index = std::distance(protein_set.begin(),std::find(protein_set.begin(), protein_set.end(), *it));
peptide_protein_map.push_back(std::make_pair(peptide_set_index,protein_set_index));
}
insert_precursor_sql << "INSERT INTO PRECURSOR (ID, TRAML_ID, GROUP_LABEL, PRECURSOR_MZ, CHARGE, LIBRARY_INTENSITY, LIBRARY_RT, DECOY) VALUES (" << group_set_index << ",'" << peptide.id << "','" << peptide.getPeptideGroupLabel() << "'," << precursor_mz_map[group_set_index] << "," << peptide.getChargeState() << ",NULL," << peptide.getRetentionTime() << "," << precursor_decoy_map[group_set_index] << "); ";
insert_precursor_peptide_mapping << "INSERT INTO PRECURSOR_PEPTIDE_MAPPING (PRECURSOR_ID, PEPTIDE_ID) VALUES (" << group_set_index << "," << peptide_set_index << "); ";
}
endProgress();
// OpenSWATH: Prepare compound precursor inserts
progress = 0;
startProgress(0, targeted_exp.getCompounds().size(), "Prepare compound precursors and mapping");
for (Size i = 0; i < targeted_exp.getCompounds().size(); i++)
{
setProgress(progress++);
OpenMS::TargetedExperiment::Compound compound = targeted_exp.getCompounds()[i];
int group_set_index = std::distance(group_set.begin(),std::find(group_set.begin(), group_set.end(), compound.id));
int compound_set_index = std::distance(compound_set.begin(), std::find(compound_set.begin(), compound_set.end(), compound.id));
std::string compound_charge = "NULL"; // workaround for compounds with missing charge
if (compound.hasCharge())
{
compound_charge = String(compound.getChargeState());
}
insert_precursor_sql << "INSERT INTO PRECURSOR (ID, TRAML_ID, GROUP_LABEL, PRECURSOR_MZ, CHARGE, LIBRARY_INTENSITY, LIBRARY_RT, DECOY) VALUES (" << group_set_index << ",'" << compound.id << "',NULL," << precursor_mz_map[group_set_index] << "," << compound_charge << ",NULL,NULL" << "," << precursor_decoy_map[group_set_index] << "); ";
insert_precursor_compound_mapping << "INSERT INTO PRECURSOR_COMPOUND_MAPPING (PRECURSOR_ID, COMPOUND_ID) VALUES (" << group_set_index << "," << compound_set_index << "); ";
}
endProgress();
boost::erase(peptide_protein_map, boost::unique<boost::return_found_end>(boost::sort(peptide_protein_map)));
// OpenSWATH: Prepare peptide-protein mapping inserts
std::stringstream insert_peptide_protein_mapping;
progress = 0;
startProgress(0, peptide_protein_map.size(), "Prepare peptide - protein mapping");
for (std::vector<std::pair<int, int> >::iterator it = peptide_protein_map.begin(); it != peptide_protein_map.end(); ++it)
{
setProgress(progress++);
insert_peptide_protein_mapping << "INSERT INTO PEPTIDE_PROTEIN_MAPPING (PEPTIDE_ID, PROTEIN_ID) VALUES (" << it->first << "," << it->second << "); ";
}
endProgress();
// OpenSWATH: Prepare protein inserts
std::stringstream insert_protein_sql;
progress = 0;
startProgress(0, protein_set.size(), String("Prepare ") + protein_set.size() + " proteins");
for (Size i = 0; i < protein_set.size(); i++)
{
setProgress(progress++);
insert_protein_sql << "INSERT INTO PROTEIN (ID, PROTEIN_ACCESSION) VALUES (" << i << ",'" << protein_set[i] << "'); ";
}
endProgress();
// OpenSWATH: Prepare peptide inserts
std::stringstream insert_peptide_sql;
progress = 0;
startProgress(0, peptide_set.size(), String("Prepare ") + peptide_set.size() + " peptides");
for (std::vector<std::string>::iterator it = peptide_set.begin(); it != peptide_set.end(); ++it)
{
setProgress(progress++);
insert_peptide_sql << "INSERT INTO PEPTIDE (ID, UNMODIFIED_SEQUENCE, MODIFIED_SEQUENCE, DECOY) VALUES (" << std::distance(peptide_set.begin(),std::find(peptide_set.begin(), peptide_set.end(),*it)) << ",'" << AASequence::fromString(*it).toUnmodifiedString() << "','" << *it << "'," << 0 <<"); ";
}
endProgress();
// OpenSWATH: Prepare compound inserts
std::stringstream insert_compound_sql;
progress = 0;
startProgress(0, compound_set.size(), String("Prepare ") + compound_set.size() + " compounds");
for (std::vector<std::string>::iterator it = compound_set.begin(); it != compound_set.end(); ++it)
{
setProgress(progress++);
OpenMS::TargetedExperiment::Compound compound = targeted_exp.getCompoundByRef(*it);
insert_compound_sql << "INSERT INTO COMPOUND (ID, COMPOUND_NAME, SUM_FORMULA, SMILES, DECOY) VALUES (" << std::distance(compound_set.begin(),std::find(compound_set.begin(), compound_set.end(),*it)) << ",'" << compound.id << "','" << compound.molecular_formula << "','" << compound.smiles_string << "'," << 0 <<"); ";
}
endProgress();
std::cout << "Write PQP file" << std::endl;
sqlite3_exec(db, "BEGIN TRANSACTION", NULL, NULL, &zErrMsg);
// Execute SQL insert statement
std::string insert_protein_sql_str = insert_protein_sql.str();
rc = sqlite3_exec(db, insert_protein_sql_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Execute SQL insert statement
std::string insert_peptide_protein_mapping_str = insert_peptide_protein_mapping.str();
rc = sqlite3_exec(db, insert_peptide_protein_mapping_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Execute SQL insert statement
std::string insert_peptide_sql_str = insert_peptide_sql.str();
rc = sqlite3_exec(db, insert_peptide_sql_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Execute SQL insert statement
std::string insert_compound_sql_str = insert_compound_sql.str();
rc = sqlite3_exec(db, insert_compound_sql_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Execute SQL insert statement
std::string insert_precursor_peptide_mapping_str = insert_precursor_peptide_mapping.str();
rc = sqlite3_exec(db, insert_precursor_peptide_mapping_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Execute SQL insert statement
std::string insert_precursor_compound_mapping_str = insert_precursor_compound_mapping.str();
rc = sqlite3_exec(db, insert_precursor_compound_mapping_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Execute SQL insert statement
std::string insert_precursor_sql_str = insert_precursor_sql.str();
rc = sqlite3_exec(db, insert_precursor_sql_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Execute SQL insert statement
std::string insert_transition_sql_str = insert_transition_sql.str();
rc = sqlite3_exec(db, insert_transition_sql_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Execute SQL insert statement
std::string insert_transition_peptide_mapping_sql_str = insert_transition_peptide_mapping_sql.str();
rc = sqlite3_exec(db, insert_transition_peptide_mapping_sql_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
// Execute SQL insert statement
std::string insert_transition_precursor_mapping_sql_str = insert_transition_precursor_mapping_sql.str();
rc = sqlite3_exec(db, insert_transition_precursor_mapping_sql_str.c_str(), callback, 0, &zErrMsg);
if ( rc != SQLITE_OK )
{
sqlite3_free(zErrMsg);
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
zErrMsg);
}
sqlite3_exec(db, "END TRANSACTION", NULL, NULL, &zErrMsg);
sqlite3_close(db);
}
