/// <summary>
/// Store PSM Data
/// </summary>
/// <param name="result"></param>
/// <param name="reader"></param>
/// <param name="specProb"></param>
protected void StorePsmData(Evidence result, clsPHRPReader reader, double specProb)
{
result.Charge = reader.CurrentPSM.Charge;
result.CleanPeptide = reader.CurrentPSM.PeptideCleanSequence;
result.SeqWithNumericMods = reader.CurrentPSM.PeptideWithNumericMods;
result.MonoisotopicMass = reader.CurrentPSM.PeptideMonoisotopicMass;
result.ObservedMonoisotopicMass = reader.CurrentPSM.PrecursorNeutralMass;
result.MultiProteinCount = (short)reader.CurrentPSM.Proteins.Count;
result.Scan = reader.CurrentPSM.ScanNumber;
result.Sequence = reader.CurrentPSM.Peptide;
result.Mz =
clsPeptideMassCalculator.ConvoluteMass(reader.CurrentPSM.PrecursorNeutralMass, 0,
reader.CurrentPSM.Charge);
result.SpecProb = specProb;
result.DelM = Convert.ToDouble(reader.CurrentPSM.MassErrorDa);
result.ModificationCount = (short)reader.CurrentPSM.ModifiedResidues.Count;
result.PeptideInfo = new TargetPeptideInfo
{
Peptide = result.Sequence,
CleanPeptide = result.CleanPeptide,
PeptideWithNumericMods = result.SeqWithNumericMods
};
if (reader.CurrentPSM.MassErrorPPM.Length != 0)
{
result.DelMPpm = Convert.ToDouble(reader.CurrentPSM.MassErrorPPM);
}
result.SeqInfoMonoisotopicMass = result.MonoisotopicMass;
StoreProteinInfo(reader, result);
if (result.ModificationCount != 0)
{
foreach (var info in reader.CurrentPSM.ModifiedResidues)
{
result.ModificationDescription += info.ModDefinition.MassCorrectionTag + ":" + info.ResidueLocInPeptide + " ";
var ptm = new PostTranslationalModification
{
Location = info.ResidueLocInPeptide,
Mass = info.ModDefinition.ModificationMass,
Formula = info.ModDefinition.MassCorrectionTag,
Name = info.ModDefinition.MassCorrectionTag
};
result.Ptms.Add(ptm);
}
var encodedSeq = result.Sequence[0] + ".";
int j = 0;
foreach (var ptm in result.Ptms)
{
for (; j < ptm.Location; j++)
{
encodedSeq = encodedSeq + result.CleanPeptide[j];
}
encodedSeq += "[" + ((ptm.Mass > 0)? "+":"-") + ptm.Formula + "]";
}
for (; j < result.CleanPeptide.Length; j++)
{
encodedSeq += result.CleanPeptide[j];
}
encodedSeq += "." + result.Sequence.Last();
result.EncodedNonNumericSequence = encodedSeq;
}
else
{
result.EncodedNonNumericSequence = result.Sequence;
}
}
private void RetrieveDataFromTextFiles(string directory)
{
using (var reader = new StreamReader(directory + "tempModInfo.txt"))
{
reader.ReadLine();
var row = reader.ReadLine();
while (!string.IsNullOrEmpty(row))
{
var rowPieces = row.Split(m_separator);
m_modTagsToModMass.Add(rowPieces[0],
new Tuple <double, string>(Convert.ToDouble(rowPieces[1]), rowPieces[2]));
row = reader.ReadLine();
}
}
var ptmId = 1;
var targetId = 1;
var ctToPtmId = 1;
using (var reader = new StreamReader(directory + "tempMassTags.txt"))
{
reader.ReadLine();
var row = reader.ReadLine();
while (!string.IsNullOrEmpty(row))
{
var rowPieces = row.Split(m_separator);
var target = new ConsensusTarget();
target.Id = targetId++;
var quote = "";
var unescapedPiece = rowPieces[14].Replace("\"\"", quote);
var sequence = rowPieces[1];
if (unescapedPiece != "")
{
var unquotedPiece = unescapedPiece.Substring(1, rowPieces[14].Length - 2);
var mods = unquotedPiece.Split(',');
foreach (var mod in mods)
{
var modPieces = mod.Split(':');
var modMass = m_modTagsToModMass[modPieces[0]].Item1;
var ptm = new PostTranslationalModification();
ptm.Name = modPieces[0];
if (!m_ptmDictionary.ContainsKey(ptm.Name))
{
ptm.Mass = modMass;
ptm.Id = ptmId++;
ptm.Formula = m_modTagsToModMass[modPieces[0]].Item2;
m_ptmDictionary.Add(ptm.Name, ptm);
}
target.Ptms.Add(m_ptmDictionary[ptm.Name]);
ptm.Location = Convert.ToInt32(modPieces[1]);
var ctToPtm = new ConsensusPtmPair
{
ConsensusId = target.Id,
PtmId = m_ptmDictionary[ptm.Name].Id,
Location = ptm.Location,
Id = ctToPtmId++
};
m_consensusTargetToPtmDict[ctToPtm.Id] = ctToPtm;
}
target.ModificationDescription = unquotedPiece;
}
var fullSequence = sequence;
var backPtms = target.Ptms.OrderByDescending(x => x.Location);
foreach (var ptm in backPtms)
{
if (ptm.Location == rowPieces[1].Length)
{
rowPieces[1] += ptm.Mass.ToString();
}
else
{
rowPieces[1] = fullSequence.Insert(ptm.Location, ptm.Mass.ToString());
}
}
target.EncodedNumericSequence = rowPieces[1];
target.Sequence = fullSequence;
target.TheoreticalMonoIsotopicMass = Convert.ToDouble(rowPieces[2]);
target.MultiProteinCount = Convert.ToInt16(rowPieces[4]);
target.ModificationCount = Convert.ToInt16(rowPieces[13]);
m_idToMassTagDict.Add(Convert.ToInt32(rowPieces[0]), row);
m_idToConensusTargetDict.Add(Convert.ToInt32(rowPieces[0]), target);
row = reader.ReadLine();
}
}
using (var reader = new StreamReader(directory + "tempMassTagsNet.txt"))
{
reader.ReadLine();
var row = reader.ReadLine();
while (!string.IsNullOrEmpty(row))
{
var rowPieces = row.Split(m_separator);
var id = Convert.ToInt32(rowPieces[0]);
m_idToConensusTargetDict[id].PredictedNet = Convert.ToDouble(rowPieces[7]);
m_idToConensusTargetDict[id].StdevNet = Convert.ToDouble(rowPieces[5]);
m_idToConensusTargetDict[id].AverageNet = Convert.ToDouble(rowPieces[3]);
row = reader.ReadLine();
}
}
var proteinId = 1;
using (var reader = new StreamReader(directory + "tempProteins.txt"))
{
reader.ReadLine();
var row = reader.ReadLine();
while (!string.IsNullOrEmpty(row))
{
var rowPieces = row.Split(m_separator);
var unquotedPiece = rowPieces[1].Substring(1, rowPieces[1].Length - 2);
var prot = new ProteinInformation {
Id = proteinId++, ProteinName = unquotedPiece
};
m_idToProteinDict[Convert.ToInt32(rowPieces[0])] = prot;
row = reader.ReadLine();
}
}
var cppId = 1;
using (var reader = new StreamReader(directory + "tempMassTagToProteins.txt"))
{
reader.ReadLine();
var row = reader.ReadLine();
while (!string.IsNullOrEmpty(row))
{
var rowPieces = row.Split(m_separator);
var mt_id = Convert.ToInt32(rowPieces[0]);
var prot_id = Convert.ToInt32(rowPieces[2]);
var ctToProt = new ConsensusProteinPair();
ctToProt.CleavageState = Convert.ToInt16(rowPieces[3]);
ctToProt.ResidueStart = Convert.ToInt32(rowPieces[6]);
ctToProt.ResidueEnd = Convert.ToInt32(rowPieces[7]);
ctToProt.TerminusState = Convert.ToInt16(rowPieces[9]);
ctToProt.ConsensusId = m_idToConensusTargetDict[mt_id].Id;
ctToProt.ProteinId = m_idToProteinDict[prot_id].Id;
m_ctToProtDict[cppId] = ctToProt;
cppId++;
row = reader.ReadLine();
}
}
var totalCharges = 0;
var evId = 1;
using (var reader = new StreamReader(directory + "tempPeptides.txt"))
{
reader.ReadLine();
var row = reader.ReadLine();
while (!string.IsNullOrEmpty(row))
{
var rowPieces = row.Split(m_separator);
var id = Convert.ToInt32(rowPieces[0]);
if (!m_idToChargeAndPeptide.ContainsKey(id))
{
m_idToChargeAndPeptide[id] = new Tuple <string, List <short> >(rowPieces[1], new List <short>());
m_idToChargeAndPeptide[id].Item2.Add(Convert.ToInt16(rowPieces[2]));
m_idToConensusTargetDict[id].Sequence = rowPieces[1][0] + "." +
m_idToConensusTargetDict[id].Sequence + "." +
rowPieces[1][rowPieces[1].Length - 1];
m_idToConensusTargetDict[id].CleanSequence = m_idToConensusTargetDict[id].Sequence;
m_idToConensusTargetDict[id].Charges.Add(Convert.ToInt16(rowPieces[2]));
totalCharges++;
}
if (!m_idToChargeAndPeptide[id].Item2.Contains(Convert.ToInt16(rowPieces[2])))
{
m_idToChargeAndPeptide[id].Item2.Add(Convert.ToInt16(rowPieces[2]));
m_idToConensusTargetDict[id].Charges.Add(Convert.ToInt16(rowPieces[2]));
totalCharges++;
}
var ctId = m_idToConensusTargetDict[id].Id;
var ev = new Evidence();
ev.Id = evId++;
ev.Charge = Convert.ToInt16(rowPieces[2]);
ev.Sequence = m_idToConensusTargetDict[id].CleanSequence;
ev.Scan = Convert.ToInt32(rowPieces[3]);
ev.DelMPpm = Convert.ToDouble(rowPieces[4]);
ev.ObservedNet = Convert.ToDouble(rowPieces[5]);
ev.ObservedMonoisotopicMass = Convert.ToDouble(rowPieces[6]);
ev.Mz = ev.ObservedMonoisotopicMass / ev.Charge;
ev.NetShift = 0;
ev.DelM = ev.DelMPpm / 1000000;
ev.Parent = m_idToConensusTargetDict[id];
m_evidenceDict[evId] = ev;
if (!m_ctToEvidenceMap.ContainsKey(ctId))
{
m_ctToEvidenceMap[ctId] = new List <int>();
}
m_ctToEvidenceMap[ctId].Add(evId);
row = reader.ReadLine();
}
}
}
/// <summary>
/// Map the results of a MZIdentML read to MSGF+
/// </summary>
/// <param name="results">Object to populate with the results of the Mapping</param>
/// <param name="path">Path to MZIdentML file</param>
private void MapToMsgf(List <MsgfPlusResult> results, string path)
{
var filter = new MsgfPlusTargetFilter(ReaderOptions);
var cleavageStateCalculator = new clsPeptideCleavageStateCalculator();
var i = 0;
var total = m_specItems.Count;
// Go through each Spectrum ID and map it to an MSGF+ result
foreach (var item in m_specItems)
{
i++;
if (i % 500 == 0)
{
UpdateProgress((100 * ((float)i / total)));
}
// Skip this PSM if it doesn't pass the import filters
// Note that qValue is basically FDR
double qValue = item.Value.QValue;
double specProb = item.Value.SpecEv;
if (filter.ShouldFilter(qValue, specProb))
{
continue;
}
if (item.Value.PepEvidence.Count == 0)
{
continue;
}
var evidence = item.Value.PepEvidence[0];
var result = new MsgfPlusResult
{
AnalysisId = i,
Charge = Convert.ToInt16(item.Value.Charge),
CleanPeptide = item.Value.Peptide.Sequence,
SeqWithNumericMods = null,
MonoisotopicMass = clsPeptideMassCalculator.ConvoluteMass(item.Value.CalMz, item.Value.Charge, 0),
ObservedMonoisotopicMass = clsPeptideMassCalculator.ConvoluteMass(item.Value.ExperimentalMz, item.Value.Charge, 0),
MultiProteinCount = Convert.ToInt16(item.Value.PepEvCount),
Scan = item.Value.ScanNum,
Sequence = evidence.Pre + "." + item.Value.Peptide.Sequence + "." + evidence.Post,
Mz = 0,
SpecProb = specProb,
DelM = 0,
ModificationCount = Convert.ToInt16(item.Value.Peptide.Mods.Count)
};
// Populate some mass related items
result.DelM = result.ObservedMonoisotopicMass - result.MonoisotopicMass;
result.DelMPpm = clsPeptideMassCalculator.MassToPPM(result.DelM, result.ObservedMonoisotopicMass);
// We could compute m/z:
// Mz = clsPeptideMassCalculator.ConvoluteMass(result.ObservedMonoisotopicMass, 0, result.Charge);
// But it's stored in the mzid file, so we'll use that
result.Mz = item.Value.ExperimentalMz;
StoreDatasetInfo(result, path);
result.DataSet.Tool = LcmsIdentificationTool.MZIdentML;
// Populate items specific to the MSGF+ results (stored as mzid)
result.Reference = evidence.DbSeq.Accession;
var eCleavageState = cleavageStateCalculator.ComputeCleavageState(item.Value.Peptide.Sequence, evidence.Pre, evidence.Post);
result.NumTrypticEnds = clsPeptideCleavageStateCalculator.CleavageStateToShort(eCleavageState);
result.DeNovoScore = item.Value.DeNovoScore;
result.MsgfScore = item.Value.RawScore;
result.SpecEValue = item.Value.SpecEv;
result.RankSpecEValue = item.Value.Rank;
result.EValue = item.Value.EValue;
result.QValue = qValue;
result.DiscriminantValue = qValue;
result.PepQValue = item.Value.PepQValue;
result.IsotopeError = item.Value.IsoError;
if (result.ModificationCount > 0)
{
var j = 0;
var numModSeq = evidence.Pre + ".";
var encodedSeq = numModSeq;
foreach (var mod in item.Value.Peptide.Mods)
{
var ptm = new PostTranslationalModification
{
Location = mod.Key,
Mass = mod.Value.Mass,
Formula = UniModData.ModList[mod.Value.Tag].Formula.ToString(),
Name = UniModData.ModList[mod.Value.Tag].Title
};
result.Ptms.Add(ptm);
for (; j < ptm.Location; j++)
{
numModSeq = numModSeq + item.Value.Peptide.Sequence[j];
encodedSeq = encodedSeq + item.Value.Peptide.Sequence[j];
}
numModSeq += (ptm.Mass > 0) ? "+" : "-";
numModSeq = numModSeq + ptm.Mass;
encodedSeq += "[" + ((ptm.Mass > 0)? "+":"-") + ptm.Formula + "]";
}
for (; j < item.Value.Peptide.Sequence.Length; j++)
{
numModSeq = numModSeq + item.Value.Peptide.Sequence[j];
encodedSeq += item.Value.Peptide.Sequence[j];
}
numModSeq = numModSeq + "." + evidence.Post;
encodedSeq += "." + evidence.Post;
result.SeqWithNumericMods = numModSeq;
result.EncodedNonNumericSequence = encodedSeq;
}
else
{
result.SeqWithNumericMods = result.Sequence;
result.EncodedNonNumericSequence = result.Sequence;
}
result.PeptideInfo = new TargetPeptideInfo
{
Peptide = result.Sequence,
CleanPeptide = result.CleanPeptide,
PeptideWithNumericMods = result.SeqWithNumericMods
};
result.SeqInfoMonoisotopicMass = result.MonoisotopicMass;
result.ModificationDescription = null;
foreach (var thing in item.Value.PepEvidence)
{
var protein = new ProteinInformation
{
ProteinName = thing.DbSeq.Accession,
ResidueStart = thing.Start,
ResidueEnd = thing.End
};
ComputeTerminusState(evidence, result.NumTrypticEnds, protein);
result.Proteins.Add(protein);
}
if (result.ModificationCount > 0)
{
foreach (var mod in item.Value.Peptide.Mods)
{
// TODO: Confirm that this is valid math (MEM thinks it may not be)
result.SeqInfoMonoisotopicMass += mod.Value.Mass;
result.ModificationDescription += mod.Value.Tag + ":" + mod.Key + " ";
}
}
results.Add(result);
}
}
private void ReadSqLite(string path)
{
// Don't read again if we just read the file
if (path == m_lastReadFile)
{
return;
}
// Reset the data
m_targetDb.ClearTargets();
m_lcmsDataDic.Clear();
//var sessionFactory = DatabaseReaderFactory.CreateSessionFactory(path);
DatabaseFactory.DatabaseFile = path;
DatabaseFactory.ReadOrAppend = true;
var sessionFactory = DatabaseFactory.CreateSessionFactory(DatabaseType.SQLite);
var readConsensus = new List <ConsensusTarget>();
var readPair = new List <ConsensusProteinPair>();
var readProt = new List <ProteinInformation>();
var readEvidence = new List <Evidence>();
var readPtms = new List <PostTranslationalModification>();
var readPtmPairs = new List <ConsensusPtmPair>();
var readOptions = new List <Options>();
var consensusDic = new Dictionary <int, ConsensusTarget>();
var consensusProtDic = new Dictionary <int, List <ConsensusProteinPair> >();
var consensusPtmDic = new Dictionary <int, List <ConsensusPtmPair> >();
var protDic = new Dictionary <int, ProteinInformation>();
var ptmDic = new Dictionary <int, PostTranslationalModification>();
using (var session = sessionFactory.OpenStatelessSession())
{
using (var transact = session.BeginTransaction())
{
session.CreateCriteria <ProteinInformation>().List(readProt);
session.CreateCriteria <ConsensusTarget>().List(readConsensus);
session.CreateCriteria <PostTranslationalModification>().List(readPtms);
session.CreateCriteria <Options>().List(readOptions);
session.CreateCriteria <ConsensusProteinPair>().List(readPair);
session.CreateCriteria <ConsensusPtmPair>().List(readPtmPairs);
session.CreateCriteria <Evidence>().List(readEvidence);
transact.Commit();
}
/*
* using (var transact = session.BeginTransaction())
* {
* session.CreateCriteria<ConsensusProteinPair>().List(readPair);
* session.CreateCriteria<ConsensusPtmPair>().List(readPtmPairs);
* session.CreateCriteria<Evidence>().List(readEvidence);
* transact.Commit();
* }
*/
foreach (var consensus in readConsensus)
{
consensus.Ptms.Clear();
//consensus.Evidences.Clear();
consensus.Evidences = new List <Evidence>();
consensus.Sequence = consensus.CleanSequence;
m_targetDb.AddConsensusTarget(consensus);
consensusDic.Add(consensus.Id, consensus);
}
foreach (var pair in readPair)
{
if (!consensusProtDic.ContainsKey(pair.Consensus.Id))
{
consensusProtDic.Add(pair.Consensus.Id, new List <ConsensusProteinPair>());
}
consensusProtDic[pair.Consensus.Id].Add(pair);
}
foreach (var pair in readPtmPairs)
{
if (!consensusPtmDic.ContainsKey(pair.Target.Id))
{
consensusPtmDic.Add(pair.Target.Id, new List <ConsensusPtmPair>());
}
consensusPtmDic[pair.Target.Id].Add(pair);
}
foreach (var prot in readProt)
{
protDic.Add(prot.Id, prot);
}
foreach (var ptm in readPtms)
{
ptmDic.Add(ptm.Id, ptm);
}
foreach (var consensus in consensusPtmDic)
{
foreach (var pair in consensus.Value)
{
var ptm = new PostTranslationalModification
{
Mass = ptmDic[pair.PostTranslationalModification.Id].Mass,
Name = ptmDic[pair.PostTranslationalModification.Id].Name,
Formula = ptmDic[pair.PostTranslationalModification.Id].Formula,
Location = pair.Location,
Parent = consensusDic[pair.Target.Id]
};
consensusDic[pair.Target.Id].Ptms.Add(ptm);
}
}
foreach (var evidence in readEvidence)
{
foreach (var pair in consensusProtDic[evidence.Parent.Id])
{
var prot = protDic[pair.Protein.Id];
prot.ResidueEnd = pair.ResidueEnd;
prot.ResidueStart = pair.ResidueStart;
prot.TerminusState = (clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants)pair.TerminusState;
prot.CleavageState = (clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants)pair.CleavageState;
//prot.Id = 0;
evidence.AddProtein(prot);
consensusDic[evidence.Parent.Id].AddProtein(prot);
}
evidence.MonoisotopicMass = consensusDic[evidence.Parent.Id].TheoreticalMonoIsotopicMass;
evidence.Ptms = consensusDic[evidence.Parent.Id].Ptms;
if (!m_lcmsDataDic.ContainsKey(evidence.DataSet.Name))
{
var dataset = new LcmsDataSet(true);
m_lcmsDataDic.Add(evidence.DataSet.Name, dataset);
m_lcmsDataDic[evidence.DataSet.Name].Name = evidence.DataSet.Name;
m_lcmsDataDic[evidence.DataSet.Name].Tool = evidence.DataSet.Tool;
}
m_lcmsDataDic[evidence.DataSet.Name].Evidences.Add(evidence);
consensusDic[evidence.Parent.Id].AddEvidence(evidence);
}
}
// Set the member variable to avoid double reads.
m_lastReadFile = path;
}
