public void TestProteomeDb()
{
using (var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE))
{
string fastaPath = testFilesDir.GetTestPath("high_ipi.Human.20060111.fasta");
string protDbPath = testFilesDir.GetTestPath("test.protdb");
using (ProteomeDb proteomeDb = ProteomeDb.CreateProteomeDb(protDbPath))
{
IProgressStatus status = new ProgressStatus(string.Empty);
using (var reader = new StreamReader(fastaPath))
{
proteomeDb.AddFastaFile(reader, new SilentProgressMonitor(), ref status, true); // Delay indexing
}
// perform digestion
Digestion digestion = proteomeDb.GetDigestion();
var digestedProteins0 = digestion.GetProteinsWithSequence("EDGWVK");
Assert.IsTrue(digestedProteins0.Count >= 1);
}
}
}
public void TestProteomeDb()
{
using (var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE))
{
string fastaPath = testFilesDir.GetTestPath("high_ipi.Human.20060111.fasta");
string protDbPath = testFilesDir.GetTestPath("test.protdb");
using (ProteomeDb proteomeDb = ProteomeDb.CreateProteomeDb(protDbPath))
{
Enzyme trypsin = EnzymeList.GetDefault();
using (var reader = new StreamReader(fastaPath))
{
proteomeDb.AddFastaFile(reader, (msg, progress) => true);
}
// perform digestion
proteomeDb.Digest(new ProteaseImpl(trypsin), (msg, progress) => true);
Digestion digestion = proteomeDb.GetDigestion(trypsin.Name);
var digestedProteins0 = digestion.GetProteinsWithSequencePrefix("EDGWVK", 100);
Assert.IsTrue(digestedProteins0.Count >= 1);
}
}
}
public void TestProteomeDb()
{
using (var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE))
{
string fastaPath = testFilesDir.GetTestPath("high_ipi.Human.20060111.fasta");
string protDbPath = testFilesDir.GetTestPath("test.protdb");
using (ProteomeDb proteomeDb = ProteomeDb.CreateProteomeDb(protDbPath))
{
Enzyme trypsin = EnzymeList.GetDefault();
IProgressStatus status = new ProgressStatus(string.Empty);
using (var reader = new StreamReader(fastaPath))
{
proteomeDb.AddFastaFile(reader, new SilentProgressMonitor(), ref status, true); // Delay indexing
}
// perform digestion
proteomeDb.Digest(new ProteaseImpl(trypsin), ProteomeDb.PROTDB_MAX_MISSED_CLEAVAGES, new SilentProgressMonitor(), ref status);
Digestion digestion = proteomeDb.GetDigestion(trypsin.Name);
var digestedProteins0 = digestion.GetProteinsWithSequencePrefix("EDGWVK", 100);
Assert.IsTrue(digestedProteins0.Count >= 1);
}
}
}
public Digestion GetDigestion(ProteomeDb proteomeDb, PeptideSettings peptideSettings)
{
return(proteomeDb.GetDigestion());
}
/// <summary>
/// Tries to match each library peptide to document settings.
/// </summary>
public void MatchAllPeptides(ILongWaitBroker broker)
{
_chargeSettingsMap = new AdductMap <SrmSettings>();
// Build a dictionary mapping sequence to proteins because getting this information is slow.
var dictSequenceProteins = new Dictionary <string, IList <ProteinInfo> >();
var dictNewNodePeps = new Dictionary <PeptideSequenceModKey, PeptideMatch>();
PeptideMatches = null;
MatchedPeptideCount = 0;
int peptides = 0;
int totalPeptides = _libraryPepInfos.Count;
ProteomeDb proteomeDb = null;
IStatelessSession session = null;
try
{
foreach (ViewLibraryPepInfo pepInfo in _libraryPepInfos)
{
if (broker.IsCanceled)
{
return;
}
var charge = pepInfo.Key.Adduct;
// Find the matching peptide.
var nodePepMatched = AssociateMatchingPeptide(pepInfo, charge).PeptideNode;
if (nodePepMatched != null)
{
MatchedPeptideCount++;
PeptideMatch peptideMatchInDict;
// If peptide is already in the dictionary of peptides to add, merge the children.
if (!dictNewNodePeps.TryGetValue(nodePepMatched.SequenceKey, out peptideMatchInDict))
{
IList <ProteinInfo> matchedProteins = null;
var target = nodePepMatched.Peptide.Target;
// This is only set if the user has checked the associate peptide box.
if (target.IsProteomic && _backgroundProteome != null)
{
var sequence = target.Sequence;
// We want to query the background proteome as little as possible,
// so sequences are mapped to protein lists in a dictionary.
if (!dictSequenceProteins.TryGetValue(sequence, out matchedProteins))
{
if (proteomeDb == null)
{
proteomeDb = _backgroundProteome.OpenProteomeDb(broker.CancellationToken);
session = proteomeDb.OpenStatelessSession(false);
}
var digestion = proteomeDb.GetDigestion();
if (sequence.Length >= MIN_PEPTIDE_LENGTH)
{
matchedProteins = digestion.GetProteinsWithSequence(session, sequence)
.Select(protein => new ProteinInfo(protein)).ToList();
}
if (matchedProteins == null || matchedProteins.Count > MAX_PROTEIN_MATCHES)
{
// If the peptide was too short, or matched too many proteins, then
// treat it as if it was not found in any proteins.
matchedProteins = new List <ProteinInfo>();
}
dictSequenceProteins.Add(sequence, matchedProteins);
}
}
dictNewNodePeps.Add(nodePepMatched.SequenceKey,
new PeptideMatch(nodePepMatched, matchedProteins,
MatchesFilter(target, charge)));
}
else
{
PeptideDocNode nodePepInDictionary = peptideMatchInDict.NodePep;
if (!nodePepInDictionary.HasChildCharge(charge))
{
List <DocNode> newChildren = nodePepInDictionary.Children.ToList();
newChildren.AddRange(nodePepMatched.Children);
newChildren.Sort(Peptide.CompareGroups);
var key = nodePepMatched.SequenceKey;
dictNewNodePeps.Remove(key);
dictNewNodePeps.Add(key,
new PeptideMatch((PeptideDocNode)nodePepInDictionary.ChangeChildren(newChildren),
peptideMatchInDict.Proteins, peptideMatchInDict.MatchesFilterSettings));
}
}
}
peptides++;
int progressValue = (int)((peptides + 0.0) / totalPeptides * PERCENT_PEPTIDE_MATCH);
broker.ProgressValue = progressValue;
}
PeptideMatches = dictNewNodePeps;
}
finally
{
using (proteomeDb)
using (session)
{
}
}
}
public Digestion GetDigestion(ProteomeDb proteomeDb, PeptideSettings peptideSettings)
{
return(proteomeDb.GetDigestion(peptideSettings.Enzyme.Name));
}