public Digestion GetDigestion(String name) { DbDigestion digestion = GetDbDigestion(name); if (digestion == null) { return(null); } return(new Digestion(this, digestion)); }
public Digestion Digest(IProtease protease, String name, String description, ProgressMonitor progressMonitor) { DbOrganism organism; DbDigestion digestion; List <DbProtein> proteins; using (ISession session = ProteomeDb.OpenWriteSession()) { organism = GetEntity(session); session.BeginTransaction(); digestion = new DbDigestion { Name = name, Description = description, Organism = organism, MaxMissedCleavages = protease.MaxMissedCleavages }; session.Save(digestion); if (!progressMonitor.Invoke("Listing proteins", 0)) { return(null); } proteins = new List <DbProtein>(organism.Proteins); Dictionary <String, long> digestedPeptideIds = new Dictionary <string, long>(); const String sqlPeptide = "INSERT INTO ProteomeDbDigestedPeptide (Digestion, MissedCleavages, Sequence, Version) VALUES(@Digestion,@MissedCleavages,@Sequence,1);select last_insert_rowid();"; var commandPeptide = session.Connection.CreateCommand(); commandPeptide.CommandText = sqlPeptide; commandPeptide.Parameters.Add(new SQLiteParameter("@Digestion")); commandPeptide.Parameters.Add(new SQLiteParameter("@MissedCleavages")); commandPeptide.Parameters.Add(new SQLiteParameter("@Sequence")); const String sqlPeptideProtein = "INSERT INTO ProteomeDbDigestedPeptideProtein (StartIndex, Peptide, Protein, Version) VALUES(?,?,?,1);"; var commandProtein = session.Connection.CreateCommand(); commandProtein.CommandText = sqlPeptideProtein; commandProtein.Parameters.Add(new SQLiteParameter("@StartIndex")); commandProtein.Parameters.Add(new SQLiteParameter("@Peptide")); commandProtein.Parameters.Add(new SQLiteParameter("@Protein")); for (int i = 0; i < proteins.Count; i++) { if (!progressMonitor.Invoke("Digesting " + proteins.Count + " proteins", 100 * i / proteins.Count)) { return(null); } Protein protein = new Protein(this, proteins[i]); foreach (DigestedPeptide digestedPeptide in protease.Digest(protein)) { if (digestedPeptide.Sequence.Length > MAX_PEPTIDE_LENGTH) { continue; } long digestedPeptideId; if (!digestedPeptideIds.TryGetValue(digestedPeptide.Sequence, out digestedPeptideId)) { ((SQLiteParameter)commandPeptide.Parameters[0]).Value = digestion.Id; ((SQLiteParameter)commandPeptide.Parameters[1]).Value = digestedPeptide.MissedCleavages; ((SQLiteParameter)commandPeptide.Parameters[2]).Value = digestedPeptide.Sequence; digestedPeptideId = Convert.ToInt64(commandPeptide.ExecuteScalar()); digestedPeptideIds.Add(digestedPeptide.Sequence, digestedPeptideId); } ((SQLiteParameter)commandProtein.Parameters[0]).Value = digestedPeptide.Index; ((SQLiteParameter)commandProtein.Parameters[1]).Value = digestedPeptideId; ((SQLiteParameter)commandProtein.Parameters[2]).Value = proteins[i].Id; commandProtein.ExecuteNonQuery(); } } if (!progressMonitor.Invoke("Committing transaction", 99)) { return(null); } session.Transaction.Commit(); progressMonitor.Invoke( "Digested " + proteins.Count + " proteins into " + digestedPeptideIds.Count + " unique peptides", 100); return(new Digestion(this, digestion)); } }
public Digestion Digest(IProtease protease, ProgressMonitor progressMonitor) { using (ISession session = OpenWriteSession()) { DbDigestion dbDigestion = GetDbDigestion(protease.Name); HashSet <string> existingSequences = new HashSet <string>(); using (var transaction = session.BeginTransaction()) { if (dbDigestion != null) { if (dbDigestion.MaxSequenceLength >= MAX_SEQUENCE_LENGTH) { return(new Digestion(this, dbDigestion)); } if (!progressMonitor.Invoke(Resources.ProteomeDb_Digest_Listing_existing_peptides, 0)) { return(null); } IQuery query = session.CreateQuery("SELECT P.Sequence FROM " // Not L10N + typeof(DbDigestedPeptide) + " P WHERE P.Digestion = :Digestion") // Not L10N .SetParameter("Digestion", dbDigestion); // Not L10N List <String> listSequences = new List <string>(); query.List(listSequences); existingSequences.UnionWith(listSequences); dbDigestion.MaxSequenceLength = MAX_SEQUENCE_LENGTH; session.Update(dbDigestion); } else { dbDigestion = new DbDigestion { Name = protease.Name, MinSequenceLength = MIN_SEQUENCE_LENGTH, MaxSequenceLength = MAX_SEQUENCE_LENGTH, }; session.Save(dbDigestion); } if (!progressMonitor.Invoke(Resources.ProteomeDb_Digest_Listing_proteins, 0)) { return(null); } List <DbProtein> proteins = new List <DbProtein>(); session.CreateCriteria(typeof(DbProtein)).List(proteins); Dictionary <String, long> digestedPeptideIds = new Dictionary <string, long>(); const String sqlPeptide = "INSERT INTO ProteomeDbDigestedPeptide (Digestion, Sequence) VALUES(?,?);select last_insert_rowid();"; // Not L10N using (var commandPeptide = session.Connection.CreateCommand()) using (var commandProtein = session.Connection.CreateCommand()) { commandPeptide.CommandText = sqlPeptide; commandPeptide.Parameters.Add(new SQLiteParameter()); commandPeptide.Parameters.Add(new SQLiteParameter()); const String sqlPeptideProtein = "INSERT INTO ProteomeDbDigestedPeptideProtein (Peptide, Protein) VALUES(?,?);"; // Not L10N commandProtein.CommandText = sqlPeptideProtein; commandProtein.Parameters.Add(new SQLiteParameter()); commandProtein.Parameters.Add(new SQLiteParameter()); commandProtein.Parameters.Add(new SQLiteParameter()); for (int i = 0; i < proteins.Count; i++) { var proteinSequences = new HashSet <string>(); if (!progressMonitor.Invoke(string.Format(Resources.ProteomeDb_Digest_Digesting__0__proteins, proteins.Count), 100 * i / proteins.Count)) { return(null); } Protein protein = new Protein(ProteomeDbPath, proteins[i]); foreach (DigestedPeptide digestedPeptide in protease.Digest(protein)) { if (digestedPeptide.Sequence.Length < dbDigestion.MinSequenceLength) { continue; } String truncatedSequence = digestedPeptide.Sequence.Substring( 0, Math.Min(digestedPeptide.Sequence.Length, dbDigestion.MaxSequenceLength)); if (existingSequences.Contains(truncatedSequence)) { continue; } if (proteinSequences.Contains(truncatedSequence)) { continue; } proteinSequences.Add(truncatedSequence); long digestedPeptideId; if (!digestedPeptideIds.TryGetValue(truncatedSequence, out digestedPeptideId)) { ((SQLiteParameter)commandPeptide.Parameters[0]).Value = dbDigestion.Id; ((SQLiteParameter)commandPeptide.Parameters[1]).Value = truncatedSequence; digestedPeptideId = Convert.ToInt64(commandPeptide.ExecuteScalar()); digestedPeptideIds.Add(truncatedSequence, digestedPeptideId); } ((SQLiteParameter)commandProtein.Parameters[0]).Value = digestedPeptideId; ((SQLiteParameter)commandProtein.Parameters[1]).Value = protein.Id; commandProtein.ExecuteNonQuery(); } } } if (!progressMonitor.Invoke(Resources.ProteomeDb_AddFastaFile_Saving_changes, 99)) { return(null); } transaction.Commit(); AnalyzeDb(session); progressMonitor.Invoke( string.Format(Resources.ProteomeDb_Digest_Digested__0__proteins_into__1__unique_peptides, proteins.Count, digestedPeptideIds.Count), 100); } return(new Digestion(this, dbDigestion)); } }
public Digestion Digest(IProtease protease, ProgressMonitor progressMonitor) { using (ISession session = OpenWriteSession()) { DbDigestion dbDigestion = GetDbDigestion(protease.Name); HashSet<string> existingSequences = new HashSet<string>(); using (var transaction = session.BeginTransaction()) { if (dbDigestion != null) { if (dbDigestion.MaxSequenceLength >= MAX_SEQUENCE_LENGTH) { return new Digestion(this, dbDigestion); } if (!progressMonitor.Invoke(Resources.ProteomeDb_Digest_Listing_existing_peptides, 0)) { return null; } IQuery query = session.CreateQuery("SELECT P.Sequence FROM " // Not L10N + typeof(DbDigestedPeptide) + " P WHERE P.Digestion = :Digestion") // Not L10N .SetParameter("Digestion", dbDigestion); // Not L10N List<String> listSequences = new List<string>(); query.List(listSequences); existingSequences.UnionWith(listSequences); dbDigestion.MaxSequenceLength = MAX_SEQUENCE_LENGTH; session.Update(dbDigestion); } else { dbDigestion = new DbDigestion { Name = protease.Name, MinSequenceLength = MIN_SEQUENCE_LENGTH, MaxSequenceLength = MAX_SEQUENCE_LENGTH, }; session.Save(dbDigestion); } if (!progressMonitor.Invoke(Resources.ProteomeDb_Digest_Listing_proteins, 0)) { return null; } List<DbProtein> proteins = new List<DbProtein>(); session.CreateCriteria(typeof(DbProtein)).List(proteins); Dictionary<String, long> digestedPeptideIds = new Dictionary<string, long>(); const String sqlPeptide = "INSERT INTO ProteomeDbDigestedPeptide (Digestion, Sequence) VALUES(?,?);select last_insert_rowid();"; // Not L10N using (var commandPeptide = session.Connection.CreateCommand()) using (var commandProtein = session.Connection.CreateCommand()) { commandPeptide.CommandText = sqlPeptide; commandPeptide.Parameters.Add(new SQLiteParameter()); commandPeptide.Parameters.Add(new SQLiteParameter()); const String sqlPeptideProtein = "INSERT INTO ProteomeDbDigestedPeptideProtein (Peptide, Protein) VALUES(?,?);"; // Not L10N commandProtein.CommandText = sqlPeptideProtein; commandProtein.Parameters.Add(new SQLiteParameter()); commandProtein.Parameters.Add(new SQLiteParameter()); commandProtein.Parameters.Add(new SQLiteParameter()); for (int i = 0; i < proteins.Count; i++) { var proteinSequences = new HashSet<string>(); if (!progressMonitor.Invoke(string.Format(Resources.ProteomeDb_Digest_Digesting__0__proteins,proteins.Count), 100 * i / proteins.Count)) { return null; } Protein protein = new Protein(ProteomeDbPath, proteins[i]); foreach (DigestedPeptide digestedPeptide in protease.Digest(protein)) { if (digestedPeptide.Sequence.Length < dbDigestion.MinSequenceLength) { continue; } String truncatedSequence = digestedPeptide.Sequence.Substring( 0, Math.Min(digestedPeptide.Sequence.Length, dbDigestion.MaxSequenceLength)); if (existingSequences.Contains(truncatedSequence)) { continue; } if (proteinSequences.Contains(truncatedSequence)) { continue; } proteinSequences.Add(truncatedSequence); long digestedPeptideId; if (!digestedPeptideIds.TryGetValue(truncatedSequence, out digestedPeptideId)) { ((SQLiteParameter)commandPeptide.Parameters[0]).Value = dbDigestion.Id; ((SQLiteParameter)commandPeptide.Parameters[1]).Value = truncatedSequence; digestedPeptideId = Convert.ToInt64(commandPeptide.ExecuteScalar()); digestedPeptideIds.Add(truncatedSequence, digestedPeptideId); } ((SQLiteParameter)commandProtein.Parameters[0]).Value = digestedPeptideId; ((SQLiteParameter)commandProtein.Parameters[1]).Value = protein.Id; commandProtein.ExecuteNonQuery(); } } } if (!progressMonitor.Invoke(Resources.ProteomeDb_AddFastaFile_Saving_changes, 99)) { return null; } transaction.Commit(); AnalyzeDb(session); progressMonitor.Invoke( string.Format(Resources.ProteomeDb_Digest_Digested__0__proteins_into__1__unique_peptides, proteins.Count, digestedPeptideIds.Count), 100); } return new Digestion(this, dbDigestion); } }
public Digestion Digest(IProtease protease, int maxMissedCleavages, IProgressMonitor progressMonitor, ref IProgressStatus status, bool delayDbIndexing = false) { using (ISession session = OpenWriteSession()) { DbDigestion dbDigestion = GetDbDigestion(protease.Name, session); HashSet <string> existingSequences; // TODO(bspratt) - the logic around this seems fishy, investigate. Probably never actually been used. Part of fix for issue #304, probably if (dbDigestion != null) { if (dbDigestion.MaxSequenceLength >= MAX_SEQUENCE_LENGTH) { return(new Digestion(this, dbDigestion)); } if (!UpdateProgressAndCheckForCancellation(progressMonitor, ref status, Resources.ProteomeDb_Digest_Listing_existing_peptides, 0)) { return(null); } IQuery query = session.CreateQuery("SELECT P.Sequence FROM " // Not L10N + typeof(DbDigestedPeptide) + " P WHERE P.Digestion = :Digestion") // Not L10N .SetParameter("Digestion", dbDigestion); // Not L10N List <String> listSequences = new List <string>(); query.List(listSequences); existingSequences = new HashSet <string>(listSequences); dbDigestion.MaxSequenceLength = MAX_SEQUENCE_LENGTH; } else { dbDigestion = new DbDigestion { Name = protease.Name, MinSequenceLength = MIN_SEQUENCE_LENGTH, MaxSequenceLength = MAX_SEQUENCE_LENGTH, }; existingSequences = new HashSet <string>(); } if (!UpdateProgressAndCheckForCancellation(progressMonitor, ref status, Resources.ProteomeDb_Digest_Listing_proteins, 0)) { return(null); } var dbProteins = new List <DbProtein>(); session.CreateCriteria(typeof(DbProtein)).List(dbProteins); // Digest the proteins var proteinCount = dbProteins.Count; if (proteinCount == 0) { return(null); } var proteinsList = new Protein[proteinCount]; var truncatedSequences = new HashSet <string> [proteinCount]; // One hashset of sequences for each protein of interest const int N_DIGEST_THREADS = 16; // Arbitrary value - do a progress/canel check every nth protein string message = string.Format(Resources.ProteomeDb_Digest_Digesting__0__proteins, proteinCount); for (var i = 0; i < proteinCount; i += N_DIGEST_THREADS) { var endRange = Math.Min(proteinCount, i + N_DIGEST_THREADS); if (!UpdateProgressAndCheckForCancellation(progressMonitor, ref status, message, 50 * endRange / proteinCount)) { return(null); } for (int ii = i; ii < endRange; ii++) { var protein = new Protein(ProteomeDbPath, dbProteins[ii]); proteinsList[ii] = protein; } Parallel.For(i, endRange, ii => { var proteinSequences = new HashSet <string>(); // We only save the first dbDigestion.MaxSequenceLength characters of each peptide so collisions are likely truncatedSequences[ii] = proteinSequences; // One hashset of sequences for each protein of interest foreach (var digestedPeptide in protease.DigestSequence(proteinsList[ii].Sequence, maxMissedCleavages, null)) { if (digestedPeptide.Sequence.Length < dbDigestion.MinSequenceLength) { continue; } var truncatedSequence = digestedPeptide.Sequence.Substring( 0, Math.Min(digestedPeptide.Sequence.Length, dbDigestion.MaxSequenceLength)); if (!existingSequences.Contains(truncatedSequence)) { proteinSequences.Add(truncatedSequence); } } }); } // Now write to db if (!UpdateProgressAndCheckForCancellation(progressMonitor, ref status, Resources.ProteomeDb_AddFastaFile_Saving_changes, 50)) { return(null); } bool committed = true; int digestedPeptideIdsCount; try { using (var transaction = session.BeginTransaction()) { session.SaveOrUpdate(dbDigestion); Dictionary <String, long> digestedPeptideIds = new Dictionary <string, long>(); const String sqlPeptide = "INSERT INTO ProteomeDbDigestedPeptide (Digestion, Sequence) VALUES(?,?);select last_insert_rowid();"; // Not L10N using (var commandPeptide = session.Connection.CreateCommand()) using (var commandProtein = session.Connection.CreateCommand()) { commandPeptide.CommandText = sqlPeptide; commandPeptide.Parameters.Add(new SQLiteParameter()); commandPeptide.Parameters.Add(new SQLiteParameter()); const String sqlPeptideProtein = "INSERT INTO ProteomeDbDigestedPeptideProtein (Peptide, Protein) VALUES(?,?);"; // Not L10N commandProtein.CommandText = sqlPeptideProtein; commandProtein.Parameters.Add(new SQLiteParameter()); commandProtein.Parameters.Add(new SQLiteParameter()); commandProtein.Parameters.Add(new SQLiteParameter()); for (int i = 0; i < proteinCount; i++) { var protein = proteinsList[i]; if (!UpdateProgressAndCheckForCancellation(progressMonitor, ref status, message, 50 * (proteinCount + i) / proteinCount)) { return(null); } foreach (var truncatedSequence in truncatedSequences[i]) { long digestedPeptideId; if (!digestedPeptideIds.TryGetValue(truncatedSequence, out digestedPeptideId)) { ((SQLiteParameter)commandPeptide.Parameters[0]).Value = dbDigestion.Id; ((SQLiteParameter)commandPeptide.Parameters[1]).Value = truncatedSequence; digestedPeptideId = Convert.ToInt64(commandPeptide.ExecuteScalar()); digestedPeptideIds.Add(truncatedSequence, digestedPeptideId); } ((SQLiteParameter)commandProtein.Parameters[0]).Value = digestedPeptideId; ((SQLiteParameter)commandProtein.Parameters[1]).Value = protein.Id; commandProtein.ExecuteNonQuery(); } } } try { transaction.Commit(); } catch (Exception) { committed = false; } digestedPeptideIdsCount = digestedPeptideIds.Count; } } catch (Exception) { if (!committed) { return(null); // Interrupted } else { throw; } } if (committed && !delayDbIndexing) { AnalyzeDb(session); // This runs asynchronously, and interferes with writes } if (committed) { progressMonitor.UpdateProgress(new ProgressStatus(string.Format(Resources.ProteomeDb_Digest_Digested__0__proteins_into__1__unique_peptides, proteinCount, digestedPeptideIdsCount)).ChangePercentComplete(100)); } return(committed ? new Digestion(this, dbDigestion) : null); } }