ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
String target_run = getStringOption_("name");
String target_file = getStringOption_("run");
StringList qp_accs = getStringList_("qp_accessions");
//-------------------------------------------------------------
// reading input
//------------------------------------------------------------
if (target_file != "")
{
target_run = QFileInfo(QString::fromStdString(target_file)).baseName();
}
//~ !getFlag_("tables")
QcMLFile qcmlfile;
qcmlfile.load(in);
if (qp_accs.empty())
{
qp_accs.push_back("QC:0000044");
qp_accs.push_back("QC:0000047");
qp_accs.push_back("QC:0000022");
qp_accs.push_back("QC:0000038");
qp_accs.push_back("QC:0000049");
}
//TODO care for QualityParameter s
if (target_run == "")
{
for (Size i = 0; i < qp_accs.size(); ++i)
{
qcmlfile.removeAllAttachments(qp_accs[i]);
}
}
else
{
for (Size i = 0; i < qp_accs.size(); ++i)
{
qcmlfile.removeAttachment(target_run,qp_accs[i]);
}
}
qcmlfile.store(out);
return EXECUTION_OK;
}
void addBoxPlotQPs(std::map<String,String> nums, std::map<String,String> nams, String set, QcMLFile& qcmlfile)
{
for (std::map<String, String >::const_iterator it = nums.begin(); it != nums.end(); ++it)
{
QcMLFile::QualityParameter qp;
qp.name = nams[it->first]; ///< Name
qp.id = set + it->first; ///< Identifier
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = it->first;
qp.value = it->second;
qcmlfile.addSetQualityParameter(set, qp);
}
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
String target_qp = getStringOption_("qp_att_acc");
String target_acc = getStringOption_("cv_acc");
String target_run = getStringOption_("name");
String target_file = getStringOption_("run");
String plot_file = getStringOption_("plot");
String tab = getStringOption_("table");
//-------------------------------------------------------------
// fetch vocabularies
//------------------------------------------------------------
ControlledVocabulary cv;
cv.loadFromOBO("PSI-MS", File::find("/CV/psi-ms.obo"));
cv.loadFromOBO("QC", File::find("/CV/qc-cv.obo"));
//-------------------------------------------------------------
// reading input
//------------------------------------------------------------
if (target_file != "")
{
target_run = QFileInfo(QString::fromStdString(target_file)).baseName();
}
QcMLFile qcmlfile;
if (in != "")
{
qcmlfile.load(in);
}
if (target_run == "")
{
//~ check if only one run in file
std::vector<String> nas;
qcmlfile.getRunNames(nas);
if (nas.size() == 1)
{
target_run = nas.front();
}
else
{
cerr << "Error: You have to give at least one of the following parameter (in ascending precedence): name, run. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
}
QFile f(plot_file.c_str());
String plot_b64;
if (f.open(QIODevice::ReadOnly))
{
QByteArray ba = f.readAll();
f.close();
plot_b64 = String(QString(ba.toBase64()));
}
QcMLFile::Attachment at;
at.cvAcc = target_acc;
at.id = String(UniqueIdGenerator::getUniqueId());
at.cvRef = "QC"; //TODO assign right cv reference
if (plot_b64 != "" || tab != "")
{
if (plot_b64 != "")
{
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(target_acc);
at.name = term.name; ///< Name
//~ at.unitRef; //TODO MIME type
//~ at.unitAcc;
}
catch (...)
{
cerr << "Error: You have to give the accession of a existing cv term. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
at.binary = plot_b64;
}
else if (tab != "")
{
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(target_acc);
at.name = term.name; ///< Name
//~ at.unitRef; //TODO MIME type
//~ at.unitAcc;
}
catch (...)
{
cerr << "Error: You have to give the accession of a existing cv term. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
CsvFile csv_file(tab);
if (csv_file.size()>1)
{
StringList li;
csv_file.getRow(0, li);
for (Size i = 0; i < li.size(); ++i)
{
at.colTypes.push_back(li[i]);
}
for (UInt i = 1; i < csv_file.size(); ++i)
{
StringList li;
std::vector<String> v;
csv_file.getRow(i, li);
//TODO throw error if li.size() != at.colTypes.size()
for (Size i = 0; i < li.size(); ++i)
{
v.push_back(li[i]);
}
at.tableRows.push_back(v);
}
}
}
else
{
cerr << "Error: Nothing valid to attach. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
std::vector<String> ids;
qcmlfile.existsRunQualityParameter(target_run, target_qp, ids);
if (!ids.empty())
{
at.qualityRef = ids.front();
qcmlfile.addRunAttachment(target_run, at);
}
else
{
qcmlfile.existsSetQualityParameter(target_run, target_qp, ids);
if (!ids.empty())
{
at.qualityRef = ids.front();
qcmlfile.addSetAttachment(target_run, at);
}
else
{
cerr << "Error: You have to give the accession of a existing cv term to attacht to. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
}
}
qcmlfile.store(out);
return EXECUTION_OK;
}
ExitCodes main_(int, const char**)
{
vector<ProteinIdentification> prot_ids;
vector<PeptideIdentification> pep_ids;
ProteinHit temp_protein_hit;
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String inputfile_id = getStringOption_("id");
String inputfile_feature = getStringOption_("feature");
String inputfile_consensus = getStringOption_("consensus");
String inputfile_raw = getStringOption_("in");
String outputfile_name = getStringOption_("out");
//~ bool Ms1(getFlag_("MS1"));
//~ bool Ms2(getFlag_("MS2"));
bool remove_duplicate_features(getFlag_("remove_duplicate_features"));
//-------------------------------------------------------------
// fetch vocabularies
//------------------------------------------------------------
ControlledVocabulary cv;
cv.loadFromOBO("PSI-MS", File::find("/CV/psi-ms.obo"));
cv.loadFromOBO("QC", File::find("/CV/qc-cv.obo"));
QcMLFile qcmlfile;
//-------------------------------------------------------------
// MS aqiusition
//------------------------------------------------------------
String base_name = QFileInfo(QString::fromStdString(inputfile_raw)).baseName();
cout << "Reading mzML file..." << endl;
MzMLFile mz_data_file;
MSExperiment<Peak1D> exp;
MzMLFile().load(inputfile_raw, exp);
//---prep input
exp.sortSpectra();
UInt min_mz = std::numeric_limits<UInt>::max();
UInt max_mz = 0;
std::map<Size, UInt> mslevelcounts;
qcmlfile.registerRun(base_name,base_name); //TODO use UIDs
//---base MS aquisition qp
String msaq_ref = base_name + "_msaq";
QcMLFile::QualityParameter qp;
qp.id = msaq_ref; ///< Identifier
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000004";
try
{
//~ const ControlledVocabulary::CVTerm& test = cv.getTermByName("MS aquisition result details");
//~ cout << test.name << test.id << endl;
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
//~ const ControlledVocabulary::CVTerm& term = cv.getTerm("0000004");
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "mzML file"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
//---file origin qp
qp = QcMLFile::QualityParameter();
qp.name = "mzML file"; ///< Name
qp.id = base_name + "_run_name"; ///< Identifier
qp.cvRef = "MS"; ///< cv reference
qp.cvAcc = "MS:1000577";
qp.value = base_name;
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.name = "instrument model"; ///< Name
qp.id = base_name + "_instrument_name"; ///< Identifier
qp.cvRef = "MS"; ///< cv reference
qp.cvAcc = "MS:1000031";
qp.value = exp.getInstrument().getName();
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.name = "completion time"; ///< Name
qp.id = base_name + "_date"; ///< Identifier
qp.cvRef = "MS"; ///< cv reference
qp.cvAcc = "MS:1000747";
qp.value = exp.getDateTime().getDate();
qcmlfile.addRunQualityParameter(base_name, qp);
//---precursors at
QcMLFile::Attachment at;
at.cvRef = "QC"; ///< cv reference
at.cvAcc = "QC:0000044";
at.qualityRef = msaq_ref;
at.id = base_name + "_precursors"; ///< Identifier
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(at.cvAcc);
at.name = term.name; ///< Name
}
catch (...)
{
at.name = "precursors"; ///< Name
}
at.colTypes.push_back("MS:1000894_[sec]"); //RT
at.colTypes.push_back("MS:1000040"); //MZ
for (Size i = 0; i < exp.size(); ++i)
{
mslevelcounts[exp[i].getMSLevel()]++;
if (exp[i].getMSLevel() == 2)
{
if (exp[i].getPrecursors().front().getMZ() < min_mz)
{
min_mz = exp[i].getPrecursors().front().getMZ();
}
if (exp[i].getPrecursors().front().getMZ() > max_mz)
{
max_mz = exp[i].getPrecursors().front().getMZ();
}
std::vector<String> row;
row.push_back(exp[i].getRT());
row.push_back(exp[i].getPrecursors().front().getMZ());
at.tableRows.push_back(row);
}
}
qcmlfile.addRunAttachment(base_name, at);
//---aquisition results qp
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000006"; ///< cv accession for "aquisition results"
qp.id = base_name + "_ms1aquisition"; ///< Identifier
qp.value = String(mslevelcounts[1]);
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "number of ms1 spectra"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000007"; ///< cv accession for "aquisition results"
qp.id = base_name + "_ms2aquisition"; ///< Identifier
qp.value = String(mslevelcounts[2]);
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "number of ms2 spectra"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000008"; ///< cv accession for "aquisition results"
qp.id = base_name + "_Chromaquisition"; ///< Identifier
qp.value = String(exp.getChromatograms().size());
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "number of chromatograms"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
at = QcMLFile::Attachment();
at.cvRef = "QC"; ///< cv reference
at.cvAcc = "QC:0000009";
at.qualityRef = msaq_ref;
at.id = base_name + "_mzrange"; ///< Identifier
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(at.cvAcc);
at.name = term.name; ///< Name
}
catch (...)
{
at.name = "MS MZ aquisition ranges"; ///< Name
}
at.colTypes.push_back("QC:0000010"); //MZ
at.colTypes.push_back("QC:0000011"); //MZ
std::vector<String> rowmz;
rowmz.push_back(String(min_mz));
rowmz.push_back(String(max_mz));
at.tableRows.push_back(rowmz);
qcmlfile.addRunAttachment(base_name, at);
at = QcMLFile::Attachment();
at.cvRef = "QC"; ///< cv reference
at.cvAcc = "QC:0000012";
at.qualityRef = msaq_ref;
at.id = base_name + "_rtrange"; ///< Identifier
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(at.cvAcc);
at.name = term.name; ///< Name
}
catch (...)
{
at.name = "MS RT aquisition ranges"; ///< Name
}
at.colTypes.push_back("QC:0000013"); //MZ
at.colTypes.push_back("QC:0000014"); //MZ
std::vector<String> rowrt;
rowrt.push_back(String(exp.begin()->getRT()));
rowrt.push_back(String(exp.getSpectra().back().getRT()));
at.tableRows.push_back(rowrt);
qcmlfile.addRunAttachment(base_name, at);
//---ion current stability ( & tic ) qp
at = QcMLFile::Attachment();
at.cvRef = "QC"; ///< cv reference
at.cvAcc = "QC:0000022";
at.qualityRef = msaq_ref;
at.id = base_name + "_tics"; ///< Identifier
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(at.cvAcc);
at.name = term.name; ///< Name
}
catch (...)
{
at.name = "MS TICs"; ///< Name
}
at.colTypes.push_back("MS:1000894_[sec]");
at.colTypes.push_back("MS:1000285");
UInt max = 0;
Size below_10k = 0;
for (Size i = 0; i < exp.size(); ++i)
{
if (exp[i].getMSLevel() == 1)
{
UInt sum = 0;
for (Size j = 0; j < exp[i].size(); ++j)
{
sum += exp[i][j].getIntensity();
}
if (sum > max)
{
max = sum;
}
if (sum < 10000)
{
++below_10k;
}
std::vector<String> row;
row.push_back(exp[i].getRT());
row.push_back(sum);
at.tableRows.push_back(row);
}
}
qcmlfile.addRunAttachment(base_name, at);
qp = QcMLFile::QualityParameter();
qp.id = base_name + "_ticslump"; ///< Identifier
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000023";
qp.value = String((100 / exp.size()) * below_10k);
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "percentage of tic slumps"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
//-------------------------------------------------------------
// MS id
//------------------------------------------------------------
if (inputfile_id != "")
{
IdXMLFile().load(inputfile_id, prot_ids, pep_ids);
cerr << "idXML read ended. Found " << pep_ids.size() << " peptide identifications." << endl;
ProteinIdentification::SearchParameters params = prot_ids[0].getSearchParameters();
vector<String> var_mods = params.variable_modifications;
//~ boost::regex re("(?<=[KR])(?=[^P])");
String msid_ref = base_name + "_msid";
QcMLFile::QualityParameter qp;
qp.id = msid_ref; ///< Identifier
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000025";
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "MS identification result details"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
at = QcMLFile::Attachment();
at.cvRef = "QC"; ///< cv reference
at.cvAcc = "QC:0000026";
at.qualityRef = msid_ref;
at.id = base_name + "_idsetting"; ///< Identifier
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(at.cvAcc);
at.name = term.name; ///< Name
}
catch (...)
{
at.name = "MS id settings"; ///< Name
}
at.colTypes.push_back("MS:1001013"); //MS:1001013 db name MS:1001016 version MS:1001020 taxonomy
at.colTypes.push_back("MS:1001016");
at.colTypes.push_back("MS:1001020");
std::vector<String> row;
row.push_back(String(prot_ids.front().getSearchParameters().db));
row.push_back(String(prot_ids.front().getSearchParameters().db_version));
row.push_back(String(prot_ids.front().getSearchParameters().taxonomy));
at.tableRows.push_back(row);
qcmlfile.addRunAttachment(base_name, at);
UInt spectrum_count = 0;
Size peptide_hit_count = 0;
UInt runs_count = 0;
Size protein_hit_count = 0;
set<String> peptides;
set<String> proteins;
Size missedcleavages = 0;
for (Size i = 0; i < pep_ids.size(); ++i)
{
if (!pep_ids[i].empty())
{
++spectrum_count;
peptide_hit_count += pep_ids[i].getHits().size();
const vector<PeptideHit>& temp_hits = pep_ids[i].getHits();
for (Size j = 0; j < temp_hits.size(); ++j)
{
peptides.insert(temp_hits[j].getSequence().toString());
}
}
}
for (set<String>::iterator it = peptides.begin(); it != peptides.end(); ++it)
{
for (String::const_iterator st = it->begin(); st != it->end() - 1; ++st)
{
if (*st == 'K' || *st == 'R')
{
++missedcleavages;
}
}
}
for (Size i = 0; i < prot_ids.size(); ++i)
{
++runs_count;
protein_hit_count += prot_ids[i].getHits().size();
const vector<ProteinHit>& temp_hits = prot_ids[i].getHits();
for (Size j = 0; j < temp_hits.size(); ++j)
{
proteins.insert(temp_hits[j].getAccession());
}
}
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000037"; ///< cv accession
qp.id = base_name + "_misscleave"; ///< Identifier
qp.value = missedcleavages;
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "total number of missed cleavages"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000032"; ///< cv accession
qp.id = base_name + "_totprot"; ///< Identifier
qp.value = protein_hit_count;
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "total number of identified proteins"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000033"; ///< cv accession
qp.id = base_name + "_totuniqprot"; ///< Identifier
qp.value = String(proteins.size());
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "total number of uniquely identified proteins"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000029"; ///< cv accession
qp.id = base_name + "_psms"; ///< Identifier
qp.value = String(spectrum_count);
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "total number of PSM"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000030"; ///< cv accession
qp.id = base_name + "_totpeps"; ///< Identifier
qp.value = String(peptide_hit_count);
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "total number of identified peptides"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000031"; ///< cv accession
qp.id = base_name + "_totuniqpeps"; ///< Identifier
qp.value = String(peptides.size());
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "total number of uniquely identified peptides"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
at = QcMLFile::Attachment();
at.cvRef = "QC"; ///< cv reference
at.cvAcc = "QC:0000038";
at.qualityRef = msid_ref;
at.id = base_name + "_massacc"; ///< Identifier
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(at.cvAcc);
at.name = term.name; ///< Name
}
catch (...)
{
at.name = "delta ppm tables";
}
//~ delta ppm QC:0000039 RT MZ uniqueness ProteinID MS:1000885 target/decoy Score PeptideSequence MS:1000889 Annots string Similarity Charge UO:0000219 TheoreticalWeight UO:0000221 Oxidation_(M)
at.colTypes.push_back("RT");
at.colTypes.push_back("MZ");
at.colTypes.push_back("Score");
at.colTypes.push_back("PeptideSequence");
at.colTypes.push_back("Charge");
at.colTypes.push_back("TheoreticalWeight");
at.colTypes.push_back("delta_ppm");
for (UInt w = 0; w < var_mods.size(); ++w)
{
at.colTypes.push_back(String(var_mods[w]).substitute(' ', '_'));
}
std::vector<double> deltas;
//~ prot_ids[0].getSearchParameters();
for (vector<PeptideIdentification>::iterator it = pep_ids.begin(); it != pep_ids.end(); ++it)
{
if (it->getHits().size() > 0)
{
std::vector<String> row;
row.push_back(it->getRT());
row.push_back(it->getMZ());
PeptideHit tmp = it->getHits().front(); //TODO depends on score & sort
vector<UInt> pep_mods;
for (UInt w = 0; w < var_mods.size(); ++w)
{
pep_mods.push_back(0);
}
for (AASequence::ConstIterator z = tmp.getSequence().begin(); z != tmp.getSequence().end(); ++z)
{
Residue res = *z;
String temp;
if (res.getModification().size() > 0 && res.getModification() != "Carbamidomethyl")
{
temp = res.getModification() + " (" + res.getOneLetterCode() + ")";
//cout<<res.getModification()<<endl;
for (UInt w = 0; w < var_mods.size(); ++w)
{
if (temp == var_mods[w])
{
//cout<<temp;
pep_mods[w] += 1;
}
}
}
}
row.push_back(tmp.getScore());
row.push_back(tmp.getSequence().toString().removeWhitespaces());
row.push_back(tmp.getCharge());
row.push_back(String((tmp.getSequence().getMonoWeight() + tmp.getCharge() * Constants::PROTON_MASS_U) / tmp.getCharge()));
double dppm = /* std::abs */ (getMassDifference(((tmp.getSequence().getMonoWeight() + tmp.getCharge() * Constants::PROTON_MASS_U) / tmp.getCharge()), it->getMZ(), true));
row.push_back(String(dppm));
deltas.push_back(dppm);
for (UInt w = 0; w < var_mods.size(); ++w)
{
row.push_back(pep_mods[w]);
}
at.tableRows.push_back(row);
}
}
qcmlfile.addRunAttachment(base_name, at);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000040"; ///< cv accession
qp.id = base_name + "_mean_delta"; ///< Identifier
qp.value = String(OpenMS::Math::mean(deltas.begin(), deltas.end()));
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "mean delta ppm"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000041"; ///< cv accession
qp.id = base_name + "_median_delta"; ///< Identifier
qp.value = String(OpenMS::Math::median(deltas.begin(), deltas.end(), false));
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "median delta ppm"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000035"; ///< cv accession
qp.id = base_name + "_ratio_id"; ///< Identifier
qp.value = String(double(pep_ids.size()) / double(mslevelcounts[2]));
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "id ratio"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
}
//-------------------------------------------------------------
// MS quantitation
//------------------------------------------------------------
FeatureMap map;
String msqu_ref = base_name + "_msqu";
if (inputfile_feature != "")
{
FeatureXMLFile f;
f.load(inputfile_feature, map);
cout << "Read featureXML file..." << endl;
//~ UInt fiter = 0;
map.sortByRT();
map.updateRanges();
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000045"; ///< cv accession
qp.id = msqu_ref; ///< Identifier
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "MS quantification result details"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
qp = QcMLFile::QualityParameter();
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:0000046"; ///< cv accession
qp.id = base_name + "_feature_count"; ///< Identifier
qp.value = String(map.size());
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(qp.cvAcc);
qp.name = term.name; ///< Name
}
catch (...)
{
qp.name = "number of features"; ///< Name
}
qcmlfile.addRunQualityParameter(base_name, qp);
}
if (inputfile_feature != "" && !remove_duplicate_features)
{
QcMLFile::Attachment at;
at = QcMLFile::Attachment();
at.cvRef = "QC"; ///< cv reference
at.cvAcc = "QC:0000047";
at.qualityRef = msqu_ref;
at.id = base_name + "_features"; ///< Identifier
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(at.cvAcc);
at.name = term.name; ///< Name
}
catch (...)
{
at.name = "features"; ///< Name
}
at.colTypes.push_back("MZ");
at.colTypes.push_back("RT");
at.colTypes.push_back("Intensity");
at.colTypes.push_back("Charge");
at.colTypes.push_back("Quality");
at.colTypes.push_back("FWHM");
at.colTypes.push_back("IDs");
UInt fiter = 0;
map.sortByRT();
//ofstream out(outputfile_name.c_str());
while (fiter < map.size())
{
std::vector<String> row;
row.push_back(map[fiter].getMZ());
row.push_back(map[fiter].getRT());
row.push_back(map[fiter].getIntensity());
row.push_back(map[fiter].getCharge());
row.push_back(map[fiter].getOverallQuality());
row.push_back(map[fiter].getWidth());
row.push_back(map[fiter].getPeptideIdentifications().size());
fiter++;
at.tableRows.push_back(row);
}
qcmlfile.addRunAttachment(base_name, at);
}
else if (inputfile_feature != "" && remove_duplicate_features)
{
QcMLFile::Attachment at;
at = QcMLFile::Attachment();
at.cvRef = "QC"; ///< cv reference
at.cvAcc = "QC:0000047";
at.qualityRef = msqu_ref;
at.id = base_name + "_features"; ///< Identifier
try
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(at.cvAcc);
at.name = term.name; ///< Name
}
catch (...)
{
at.name = "features"; ///< Name
}
at.colTypes.push_back("MZ");
at.colTypes.push_back("RT");
at.colTypes.push_back("Intensity");
at.colTypes.push_back("Charge");
FeatureMap map, map_out;
FeatureXMLFile f;
f.load(inputfile_feature, map);
UInt fiter = 0;
map.sortByRT();
while (fiter < map.size())
{
FeatureMap map_tmp;
for (UInt k = fiter; k <= map.size(); ++k)
{
if (abs(map[fiter].getRT() - map[k].getRT()) < 0.1)
{
//~ cout << fiter << endl;
map_tmp.push_back(map[k]);
}
else
{
fiter = k;
break;
}
}
map_tmp.sortByMZ();
UInt retif = 1;
map_out.push_back(map_tmp[0]);
while (retif < map_tmp.size())
{
if (abs(map_tmp[retif].getMZ() - map_tmp[retif - 1].getMZ()) > 0.01)
{
cout << "equal RT, but mass different" << endl;
map_out.push_back(map_tmp[retif]);
}
retif++;
}
}
qcmlfile.addRunAttachment(base_name, at);
}
if (inputfile_consensus != "")
{
cout << "Reading consensusXML file..." << endl;
ConsensusXMLFile f;
ConsensusMap map;
f.load(inputfile_consensus, map);
//~ String CONSENSUS_NAME = "_consensus.tsv";
//~ String combined_out = outputfile_name + CONSENSUS_NAME;
//~ ofstream out(combined_out.c_str());
at = QcMLFile::Attachment();
qp.name = "consensuspoints"; ///< Name
//~ qp.id = base_name + "_consensuses"; ///< Identifier
qp.cvRef = "QC"; ///< cv reference
qp.cvAcc = "QC:xxxxxxxx"; ///< cv accession "featuremapper results"
at.colTypes.push_back("Native_spectrum_ID");
at.colTypes.push_back("DECON_RT_(sec)");
at.colTypes.push_back("DECON_MZ_(Th)");
at.colTypes.push_back("DECON_Intensity");
at.colTypes.push_back("Feature_RT_(sec)");
at.colTypes.push_back("Feature_MZ_(Th)");
at.colTypes.push_back("Feature_Intensity");
at.colTypes.push_back("Feature_Charge");
for (ConsensusMap::const_iterator cmit = map.begin(); cmit != map.end(); ++cmit)
{
const ConsensusFeature& CF = *cmit;
for (ConsensusFeature::const_iterator cfit = CF.begin(); cfit != CF.end(); ++cfit)
{
std::vector<String> row;
FeatureHandle FH = *cfit;
row.push_back(CF.getMetaValue("spectrum_native_id"));
row.push_back(CF.getRT()); row.push_back(CF.getMZ());
row.push_back(CF.getIntensity());
row.push_back(FH.getRT());
row.push_back(FH.getMZ());
row.push_back(FH.getCharge());
at.tableRows.push_back(row);
}
}
qcmlfile.addRunAttachment(base_name, at);
}
//-------------------------------------------------------------
// finalize
//------------------------------------------------------------
qcmlfile.store(outputfile_name);
return EXECUTION_OK;
}
ExitCodes main_(int, const char **)
{
String plot_file = "";
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
StringList in_files = getStringList_("in");
String out = getStringOption_("out");
String setname = getStringOption_("setname");
//-------------------------------------------------------------
// reading input
//-------------------------------------------------------------
QcMLFile qcmlfile;
for (Size i = 0; i < in_files.size(); ++i)
{
QcMLFile tmpfile;
tmpfile.load(in_files[i]);
qcmlfile.merge(tmpfile,setname);
}
// make #ms2 set stats
std::vector<String> ms2nums_strings;
qcmlfile.collectSetParameter(setname,"QC:0000015", ms2nums_strings);
std::vector<Int> ms2nums;
for (std::vector<String>::iterator it = ms2nums_strings.begin(); it != ms2nums_strings.end(); ++it) //transform is too ugly and errorprone
{
ms2nums.push_back(it->toInt());
}
std::sort(ms2nums.begin(), ms2nums.end());
if (ms2nums.size()>0)
{
std::map<String,String> nums;
std::map<String,String> nams;
//~ min,q1,q2,q3,max
nums["QC:0000043"] = String(ms2nums.front());
nams["QC:0000043"] = "min ms2 number";
nums["QC:0000044"] = String(OpenMS::Math::quantile(ms2nums.begin(), ms2nums.end(),25));
nams["QC:0000044"] = "Q1 ms2 number";
nums["QC:0000045"] = String(OpenMS::Math::quantile(ms2nums.begin(), ms2nums.end(),50));
nams["QC:0000045"] = "Q2 ms2 number";
nums["QC:0000046"] = String(OpenMS::Math::quantile(ms2nums.begin(), ms2nums.end(),75));
nams["QC:0000046"] = "Q3 ms2 number";
nums["QC:0000047"] = String(ms2nums.back());
nams["QC:0000047"] = "max ms2 number";
addBoxPlotQPs(nums, nams, setname, qcmlfile);
}
// make #id set stats
std::vector<String> idnums_strings;
qcmlfile.collectSetParameter(setname,"QC:0000020", idnums_strings);
std::vector<Int> idnums;
for (std::vector<String>::iterator it = idnums_strings.begin(); it != idnums_strings.end(); ++it) //transform is too ugly and errorprone
{
idnums.push_back(it->toInt());
}
std::sort(idnums.begin(), idnums.end());
if (idnums.size()>0)
{
std::map<String,String> nums;
std::map<String,String> nams;
//~ min,q1,q2,q3,max
nums["QC:0000053"] = String(idnums.front());
nams["QC:0000053"] = "min id numbers";
nums["QC:0000054"] = String(OpenMS::Math::quantile(idnums.begin(), idnums.end(),25));
nams["QC:0000054"] = "Q1 id numbers";
nums["QC:0000055"] = String(OpenMS::Math::quantile(idnums.begin(), idnums.end(),50));
nams["QC:0000055"] = "Q2 id numbers";
nums["QC:0000056"] = String(OpenMS::Math::quantile(idnums.begin(), idnums.end(),75));
nams["QC:0000056"] = "Q3 id numbers";
nums["QC:0000057"] = String(idnums.back());
nams["QC:0000057"] = "max id number";
addBoxPlotQPs(nums, nams, setname, qcmlfile);
}
qcmlfile.store(out);
return EXECUTION_OK;
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String csv = getStringOption_("out_csv");
String target_qp = getStringOption_("qp");
String target_run = getStringOption_("name");
String target_file = getStringOption_("run");
//-------------------------------------------------------------
// reading input
//------------------------------------------------------------
if (target_file != "")
{
target_run = QFileInfo(QString::fromStdString(target_file)).baseName();
}
QcMLFile qcmlfile;
qcmlfile.load(in);
if (target_run == "")
{
//~ check if only one run in file
std::vector<String> nas;
qcmlfile.getRunNames(nas);
if (nas.size() == 1)
{
target_run = nas.front();
}
else
{
cerr << "Error: You have to give at least one of the following parameter (in ascending precedence): name, run. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
}
String csv_str = "";
if (target_qp == "set id")
{
if (qcmlfile.existsSet(target_run,true))
{
csv_str = qcmlfile.exportIDstats(target_run);
}
else
{
cerr << "Error: You have to specify a existing set for this qp. " << target_run << " seems not to exist. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
}
else
{
//TODO warn when target_run is empty or not present in qcml
csv_str = qcmlfile.exportAttachment(target_run, target_qp);
}
ofstream fout(csv.c_str());
fout << csv_str << endl;
fout.close();
//~ qcmlfile.store(out);
return EXECUTION_OK;
//~ TODO export table containing all given qp
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
String mappi = getStringOption_("mapping");
String tab = getStringOption_("table");
ControlledVocabulary cv;
cv.loadFromOBO("PSI-MS", File::find("/CV/psi-ms.obo"));
cv.loadFromOBO("QC", File::find("/CV/qc-cv.obo"));
//-------------------------------------------------------------
// reading input
//------------------------------------------------------------
QcMLFile qcmlfile;
if (in != "")
{
qcmlfile.load(in);
}
if (mappi != "" && tab != "")
{
CsvFile csv_file(tab);
CsvFile map_file(mappi);
if (map_file.size()<2) //assumed that first row is the header of table and second row is the according qc
{
cerr << "Error: You have to give a mapping of your table (first row is the header of table and second row is the according qc). Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
StringList header,according;
map_file.getRow(0, header);
map_file.getRow(1, according);
if (header.size() != according.size())
{
cerr << "Error: You have to give a mapping of your table (first row is the header of table and second row is the according qc). Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
//~ std::map<String,String> mapping;
//~ std::transform( header.begin(), header.end(), according.begin(), std::inserter(mapping, mapping.end() ), std::make_pair<String,String> );
int runset_col = -1;
for (Size i = 0; i < according.size(); ++i)
{
if (!cv.exists(according[i]))
{
try
{
const ControlledVocabulary::CVTerm& term = cv.getTermByName(according[i]);
header[i] = term.name;
according[i] = term.id;
}
catch (...)
{
cerr << "Error: You have to specify a correct cv with accession or name in col "<< String(i) <<". Aborting!" << endl;
//~ cerr << "Header was: "<< header[i] << " , according value was: " << according[i] << endl;
return ILLEGAL_PARAMETERS;
}
}
else
{
const ControlledVocabulary::CVTerm& term = cv.getTerm(according[i]);
header[i] = term.name;
}
if (header[i] == "raw data file") //TODO add set name as possibility!
{
runset_col = i;
}
}
if (runset_col < 0)
{
cerr << "Error: You have to give a mapping of your table - rows to runs/sets. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
if (csv_file.size()>1)
{
StringList li;
for (Size i = 1; i < csv_file.size(); ++i)
{
StringList li;
csv_file.getRow(i, li);
if (li.size() < according.size())
{
cerr << "Error: You have to give a correct mapping of your table - row " << String(i+1) <<" is too short. Aborting!" << endl;
return ILLEGAL_PARAMETERS;
}
std::vector< QcMLFile::QualityParameter > qps;
String id;
bool set = false;
for (Size j = 0; j < li.size(); ++j)
{
if (j==runset_col)
{
if (qcmlfile.existsRun(li[j])) //TODO this only works for real run IDs
{
id = li[j];
}
else if (qcmlfile.existsSet(li[j])) //TODO this only works for real set IDs
{
id = li[j];
set = true;
}
else
{
id = li[j];
qcmlfile.registerRun(id,id);
//TODO warn that if this was supposed to be a set - now it is not!
}
}
QcMLFile::QualityParameter def;
def.name = header[j]; ///< Name
def.id = String(UniqueIdGenerator::getUniqueId());
def.cvRef = "QC"; ///< cv reference ('full name')
def.cvAcc = according[j];
def.value = li[j];
qps.push_back(def);
}
if (id!="")
{
for (std::vector<QcMLFile::QualityParameter>::const_iterator qit = qps.begin(); qit != qps.end(); ++qit)
{
if (!set)
{
qcmlfile.addRunQualityParameter(id, *qit);
}
else
{
qcmlfile.addSetQualityParameter(id, *qit);
}
}
}
}
}
}
qcmlfile.store(out);
return EXECUTION_OK;
}
