END_SECTION
START_SECTION(setOptions(const PeakFileOptions & options))
{
MzDataFile file;
TEST_EQUAL(file.getOptions().hasMSLevels(), false)
const PeakFileOptions o = file.getOptions();
PeakFileOptions options = o;
options.addMSLevel(1);
file.setOptions(options);
TEST_EQUAL(file.getOptions().hasMSLevels(), true)
}
ExitCodes main_(int, const char **) override
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
//input/output files
String in(getStringOption_("in"));
String out(getStringOption_("out"));
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
PeakMap exp;
MzMLFile f;
f.setLogType(log_type_);
PeakFileOptions options;
options.clearMSLevels();
options.addMSLevel(2);
f.getOptions() = options;
f.load(in, exp);
writeDebug_("Data set contains " + String(exp.size()) + " spectra", 1);
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
vector<PeptideIdentification> pep_ids;
CompNovoIdentificationCID comp_novo_id;
// set the options
Param algorithm_param = getParam_().copy("algorithm:", true);
comp_novo_id.setParameters(algorithm_param);
comp_novo_id.getIdentifications(pep_ids, exp);
algorithm_param = comp_novo_id.getParameters();
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
DateTime now = DateTime::now();
String date_string = now.get();
String identifier("CompNovoCID_" + date_string);
for (vector<PeptideIdentification>::iterator it = pep_ids.begin(); it != pep_ids.end(); ++it)
{
it->assignRanks();
it->setIdentifier(identifier);
}
vector<ProteinIdentification> prot_ids;
ProteinIdentification prot_id;
prot_id.setIdentifier(identifier);
prot_id.setDateTime(now);
StringList ms_runs;
exp.getPrimaryMSRunPath(ms_runs);
prot_id.setPrimaryMSRunPath(ms_runs);
ProteinIdentification::SearchParameters search_parameters;
search_parameters.charges = "+2-+3";
if (algorithm_param.getValue("tryptic_only").toBool())
{
search_parameters.digestion_enzyme = *(ProteaseDB::getInstance()->getEnzyme("Trypsin"));
}
else
{
search_parameters.digestion_enzyme = *(ProteaseDB::getInstance()->getEnzyme("no cleavage"));
}
search_parameters.mass_type = ProteinIdentification::MONOISOTOPIC;
search_parameters.fixed_modifications = algorithm_param.getValue("fixed_modifications");
search_parameters.variable_modifications = algorithm_param.getValue("variable_modifications");
search_parameters.missed_cleavages = (UInt)algorithm_param.getValue("missed_cleavages");
search_parameters.fragment_mass_tolerance = (double)algorithm_param.getValue("fragment_mass_tolerance");
search_parameters.precursor_mass_tolerance = (double)algorithm_param.getValue("precursor_mass_tolerance");
search_parameters.fragment_mass_tolerance_ppm = false;
search_parameters.precursor_mass_tolerance_ppm = false;
prot_id.setSearchParameters(search_parameters);
prot_id.setSearchEngineVersion("0.9beta");
prot_id.setSearchEngine("CompNovo");
prot_ids.push_back(prot_id);
IdXMLFile().store(out, prot_ids, pep_ids);
return EXECUTION_OK;
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in(getStringOption_("in"));
String id(getStringOption_("id"));
String out(getStringOption_("out"));
double fragment_mass_tolerance(getDoubleOption_("fragment_mass_tolerance"));
bool fragment_mass_unit_ppm = getStringOption_("fragment_mass_unit") == "Da" ? false : true;
Size max_peptide_len = getIntOption_("max_peptide_length");
Size max_num_perm = getIntOption_("max_num_perm");
AScore ascore;
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
vector<PeptideIdentification> pep_ids;
vector<ProteinIdentification> prot_ids;
vector<PeptideIdentification> pep_out;
IdXMLFile().load(id, prot_ids, pep_ids);
MSExperiment<> exp;
MzMLFile f;
f.setLogType(log_type_);
PeakFileOptions options;
options.clearMSLevels();
options.addMSLevel(2);
f.getOptions() = options;
f.load(in, exp);
exp.sortSpectra(true);
SpectrumLookup lookup;
lookup.readSpectra(exp.getSpectra());
for (vector<PeptideIdentification>::iterator pep_id = pep_ids.begin(); pep_id != pep_ids.end(); ++pep_id)
{
Size scan_id = lookup.findByRT(pep_id->getRT());
PeakSpectrum& temp = exp.getSpectrum(scan_id);
vector<PeptideHit> scored_peptides;
for (vector<PeptideHit>::const_iterator hit = pep_id->getHits().begin(); hit < pep_id->getHits().end(); ++hit)
{
PeptideHit scored_hit = *hit;
addScoreToMetaValues_(scored_hit, pep_id->getScoreType()); // backup score value
LOG_DEBUG << "starting to compute AScore RT=" << pep_id->getRT() << " SEQUENCE: " << scored_hit.getSequence().toString() << std::endl;
PeptideHit phospho_sites = ascore.compute(scored_hit, temp, fragment_mass_tolerance, fragment_mass_unit_ppm, max_peptide_len, max_num_perm);
scored_peptides.push_back(phospho_sites);
}
PeptideIdentification new_pep_id(*pep_id);
new_pep_id.setScoreType("PhosphoScore");
new_pep_id.setHigherScoreBetter(true);
new_pep_id.setHits(scored_peptides);
pep_out.push_back(new_pep_id);
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
IdXMLFile().store(out, prot_ids, pep_out);
return EXECUTION_OK;
}
