void IDFilter::removeUnreferencedProteinHits(const ProteinIdentification& identification, const vector<PeptideIdentification> peptide_identifications, ProteinIdentification& filtered_identification)
{
const String& run_identifier = identification.getIdentifier();
// build set of protein accessions that are referenced by peptides
set<String> proteinaccessions_with_peptides;
for (Size i = 0; i != peptide_identifications.size(); ++i)
{
// run id of protein and peptide identification must match
if (run_identifier == peptide_identifications[i].getIdentifier())
{
const vector<PeptideHit>& tmp_pep_hits = peptide_identifications[i].getHits();
// extract protein accessions of each peptide hit
for (Size j = 0; j != tmp_pep_hits.size(); ++j)
{
const std::vector<String>& protein_accessions = tmp_pep_hits[j].getProteinAccessions();
for (Size k = 0; k != protein_accessions.size(); ++k)
{
String key = protein_accessions[k];
proteinaccessions_with_peptides.insert(key);
}
}
}
}
// add all protein hits referenced by a peptide
const vector<ProteinHit>& temp_protein_hits = identification.getHits();
vector<ProteinHit> filtered_protein_hits;
for (Size j = 0; j != temp_protein_hits.size(); ++j)
{
const String& protein_accession = temp_protein_hits[j].getAccession();
if (proteinaccessions_with_peptides.find(protein_accession) != proteinaccessions_with_peptides.end())
{
filtered_protein_hits.push_back(temp_protein_hits[j]);
}
}
// copy identification
filtered_identification = identification;
// assign filtered hits to protein identification
filtered_identification.setHits(filtered_protein_hits);
}
END_SECTION
START_SECTION(void load(const String &filename, ProteinIdentification &protein_ids, PeptideIdentification &peptide_ids))
{
ProtXMLFile f;
ProteinIdentification proteins;
PeptideIdentification peptides;
String prot_file;
StringList ids = ListUtils::create<String>("16627578304933075941,13229490167902618598");
// we do this twice, just to check that members are correctly reset etc..
for (Int i=0;i<2;++i)
{
prot_file = OPENMS_GET_TEST_DATA_PATH("ProtXMLFile_input_1.protXML");
f.load(prot_file, proteins, peptides);
TEST_EQUAL(proteins.getIdentifier(), ids[i]);
TEST_EQUAL(peptides.getIdentifier(), ids[i]);
// groups
TEST_EQUAL(proteins.getProteinGroups().size(), 7);
TEST_EQUAL(proteins.getProteinGroups()[0].probability, 0.9990);
TEST_EQUAL(proteins.getProteinGroups()[0].accessions.size(), 1);
TEST_EQUAL(proteins.getProteinGroups()[3].accessions.size(), 2);
TEST_EQUAL(proteins.getProteinGroups()[3].accessions[0],
"P01876|IGHA1_HUMAN");
TEST_EQUAL(proteins.getProteinGroups()[3].accessions[1],
"P01877|IGHA2_HUMAN");
TEST_EQUAL(proteins.getProteinGroups()[6].probability, 0.2026);
TEST_EQUAL(proteins.getProteinGroups()[6].accessions.size(), 1);
TEST_EQUAL(proteins.getIndistinguishableProteins().size(), 7);
TEST_EQUAL(proteins.getIndistinguishableProteins()[0].accessions.size(), 1);
TEST_EQUAL(proteins.getIndistinguishableProteins()[3].accessions.size(), 2);
TEST_EQUAL(proteins.getIndistinguishableProteins()[3].accessions[0],
"P01876|IGHA1_HUMAN");
TEST_EQUAL(proteins.getIndistinguishableProteins()[3].accessions[1],
"P01877|IGHA2_HUMAN");
TEST_EQUAL(proteins.getIndistinguishableProteins()[6].accessions.size(), 1);
// proteins
TEST_EQUAL(proteins.getHits().size(), 9);
TEST_EQUAL(proteins.getHits()[0].getAccession(), "P02787|TRFE_HUMAN");
TEST_EQUAL(proteins.getHits()[0].getCoverage(), 8.6);
TEST_EQUAL(proteins.getHits()[0].getScore(), 0.9990);
// this one is indistinguishable... therefore it should have minimal infos
TEST_EQUAL(proteins.getHits()[6].getAccession(), "P00739|HPTR_HUMAN");
TEST_EQUAL(proteins.getHits()[6].getCoverage(), -1);
TEST_EQUAL(proteins.getHits()[6].getScore(), -1);
TEST_EQUAL(proteins.getHits()[8].getAccession(), "P04217|A1BG_HUMAN");
TEST_EQUAL(proteins.getHits()[8].getCoverage(), 2.0);
TEST_EQUAL(proteins.getHits()[8].getScore(), 0.2026);
// peptides
TEST_EQUAL(peptides.getHits().size(), 16);
AASequence aa_seq("MYLGYEYVTAIR");
TEST_EQUAL(peptides.getHits()[0].getSequence(), aa_seq);
TEST_EQUAL(peptides.getHits()[0].getCharge(), 2);
TEST_EQUAL(peptides.getHits()[0].getScore(), 0.8633);
TEST_EQUAL(peptides.getHits()[0].getProteinAccessions().size(), 1);
TEST_EQUAL(peptides.getHits()[0].getProteinAccessions()[0], "P02787|TRFE_HUMAN");
TEST_EQUAL(peptides.getHits()[0].getMetaValue("is_unique"), true);
TEST_EQUAL(peptides.getHits()[0].getMetaValue("is_contributing"), true);
// load 2 nd file and
prot_file = OPENMS_GET_TEST_DATA_PATH("ProtXMLFile_input_2.protXML");
}
}
void IDFilter::removeUnreferencedPeptideHits(const ProteinIdentification& identification,
vector<PeptideIdentification>& peptide_identifications,
bool delete_unreferenced_peptide_hits /* = false */)
{
const String& run_identifier = identification.getIdentifier();
// build set of protein accessions
set<String> all_prots;
const vector<ProteinHit>& temp_protein_hits = identification.getHits();
for (Size j = 0; j != temp_protein_hits.size(); ++j)
{
all_prots.insert(temp_protein_hits[j].getAccession());
}
vector<PeptideIdentification> filtered_peptide_identifications;
// remove peptides which are not referenced
for (Size i = 0; i != peptide_identifications.size(); ++i)
{
// run id of protein and peptide identification must match
if (run_identifier == peptide_identifications[i].getIdentifier())
{
const vector<PeptideHit>& tmp_pep_hits = peptide_identifications[i].getHits();
vector<PeptideHit> filtered_pep_hits;
// check protein accessions of each peptide hit
for (Size j = 0; j != tmp_pep_hits.size(); ++j)
{
vector<PeptideEvidence> hit_peptide_evidences = tmp_pep_hits[j].getPeptideEvidences();
vector<PeptideEvidence> valid_peptide_evidence;
for (vector<PeptideEvidence>::const_iterator pe_it = hit_peptide_evidences.begin(); pe_it != hit_peptide_evidences.end(); ++pe_it)
{
// find valid proteins
if (all_prots.find(pe_it->getProteinAccession()) != all_prots.end())
{
valid_peptide_evidence.push_back(*pe_it);
}
}
if (!valid_peptide_evidence.empty() || !delete_unreferenced_peptide_hits)
{
// if present, copy the hit
filtered_pep_hits.push_back(tmp_pep_hits[j]);
filtered_pep_hits.back().setPeptideEvidences(valid_peptide_evidence);
}
}
// if the peptide has hits, we use it
if (!filtered_pep_hits.empty())
{
filtered_peptide_identifications.push_back(peptide_identifications[i]);
filtered_peptide_identifications.back().setHits(filtered_pep_hits);
}
}
else // peptide is from another run, let it pass the filter
{
filtered_peptide_identifications.push_back(peptide_identifications[i]);
}
}
// exchange with new hits
filtered_peptide_identifications.swap(peptide_identifications);
}