public void TestWriteAccessDb(string path, int numberConsensus, int numberProteins, int numberEvidences)
{
var writer = new AccessTargetDatabaseWriter();
var options = new Options();
var database = new TargetDatabase();
var evidenceCount = 1;
for (var i = 1; i <= numberConsensus; i++)
{
var target = new ConsensusTarget {
Id = i
};
for (var k = 1; k <= numberProteins; k++)
{
var protein = new ProteinInformation
{
ProteinName = "Access_Test" + k,
CleavageState = clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.Full,
TerminusState =
clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.ProteinNTerminus
};
protein.Consensus.Add(target);
for (var j = 1; j <= numberEvidences; j++)
{
var evidence = new Evidence
{
AnalysisId = j,
Charge = 1,
Id = evidenceCount,
CleanPeptide = "MIKEDEGAN" + evidenceCount,
Sequence = "BIGBIRD" + evidenceCount,
Mz = 405,
Scan = evidenceCount++,
PeptideInfo = new TargetPeptideInfo()
};
evidence.AddProtein(protein);
target.AddEvidence(evidence);
}
target.AddProtein(protein);
target.CalculateStatistics();
}
target.TheoreticalMonoIsotopicMass = 100.0;
target.AverageNet = .6;
target.PredictedNet = .7;
database.ConsensusTargets.Add(target);
}
if (File.Exists(GetTestSuiteDataPath(path)))
{
File.Delete(GetTestSuiteDataPath(path));
}
writer.Write(database, options, GetTestSuiteDataPath(path));
}
/// <summary>
/// Store Protein Info
/// </summary>
/// <param name="reader"></param>
/// <param name="result"></param>
protected static void StoreProteinInfo(clsPHRPReader reader, Evidence result)
{
foreach (var p in reader.CurrentPSM.ProteinDetails)
{
var protein = new ProteinInformation
{
ProteinName = p.Value.ProteinName,
CleavageState = p.Value.CleavageState,
TerminusState = p.Value.TerminusState,
ResidueStart = p.Value.ResidueStart,
ResidueEnd = p.Value.ResidueEnd
};
result.Proteins.Add(protein);
}
}
public void TestWriteDatabase(string path, int numberOfTargets, int numberOfEvidences)
{
var reader = new SqLiteTargetDatabaseWriter();
var options = new Options();
var database = new TargetDatabase();
var proteinCount = 1;
var evidenceCount = 1;
for (var i = 1; i <= numberOfTargets; i++)
{
var target = new ConsensusTarget {
Id = i
};
var protein = new ProteinInformation
{
ProteinName = "SO_Test" + proteinCount++,
CleavageState = clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.Full,
TerminusState = clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.ProteinNTerminus,
};
protein.Consensus.Add(target);
for (var j = 1; j <= numberOfEvidences; j++)
{
var evidence = new Evidence
{
AnalysisId = j,
Charge = 1,
Id = evidenceCount,
CleanPeptide = "MIKEDEGAN" + evidenceCount,
Sequence = "BIGBIRD" + evidenceCount,
Mz = 405,
Scan = evidenceCount++,
PeptideInfo = new TargetPeptideInfo()
};
evidence.AddProtein(protein);
target.AddEvidence(evidence);
}
target.AddProtein(protein);
target.CalculateStatistics();
database.ConsensusTargets.Add(target);
}
reader.Write(database, options, GetTestSuiteDataPath(path));
}
public TargetDatabase ReadDb(string path)
{
// Read in the data from the access database
// put it into a text file (?)
// Read the data from the text file into program
var accApplication = new ACCESS.Application();
var pathPieces = path.Split('\\');
string directory = "";
foreach (var piece in pathPieces)
{
if (piece.Contains("."))
{
continue;
}
directory += piece;
directory += "\\";
}
accApplication.OpenCurrentDatabase(path);
accApplication.DoCmd.TransferText(TransferType: ACCESS.AcTextTransferType.acExportDelim,
TableName: "AMT", FileName: directory + "outTempAMT.txt", HasFieldNames: true);
accApplication.DoCmd.TransferText(TransferType: ACCESS.AcTextTransferType.acExportDelim,
TableName: "AMT_Proteins", FileName: directory + "outTempAMT_Proteins.txt", HasFieldNames: true);
accApplication.DoCmd.TransferText(TransferType: ACCESS.AcTextTransferType.acExportDelim,
TableName: "AMT_to_Protein_Map", FileName: directory + "outTempAMT_to_Protein_Map.txt", HasFieldNames: true);
accApplication.CloseCurrentDatabase();
accApplication.Quit();
// Put the data into its objects
// AMT stuff going in Consensus targets
// NET, MonoMass, Pred. Net, Peptide (Sequence with numeric mods), ID (can be crushed later)
// OBSERVED <-- number of times this peptide was seen in the AMT
// for <observed> times, add an evidence with the info? would make sense and would allow the stats calcs to be accurate
// Prot stuff going into ProteinInfo
// Prot name only thing important for MTDB, ID (can be crushed later)
// AMT map
// Link Consensus and Protein (ct[ct_id].protein.add(protein[prot_id]))
var consensusTargets = new Dictionary <int, ConsensusTarget>();
var proteins = new Dictionary <int, ProteinInformation>();
var ctReader = new StreamReader(directory + "outTempAMT.txt");
var protReader = new StreamReader(directory + "outTempAMT_Proteins.txt");
var mapReader = new StreamReader(directory + "outTempAMT_to_Protein_Map.txt");
// Read the headers for the files
ctReader.ReadLine();
protReader.ReadLine();
mapReader.ReadLine();
// Read the first "Data" lines from the files
var ctLine = ctReader.ReadLine();
var protLine = protReader.ReadLine();
var mapLine = mapReader.ReadLine();
while (ctLine != null)
{
var pieces = ctLine.Split(',');
var target = new ConsensusTarget
{
Id = Convert.ToInt32(pieces[0]),
TheoreticalMonoIsotopicMass = Convert.ToDouble(pieces[1]),
AverageNet = Convert.ToDouble(pieces[2]),
PredictedNet = Convert.ToDouble(pieces[3]),
EncodedNumericSequence = pieces[6]
};
var totalEvidences = Convert.ToInt32(pieces[4]);
var normScore = Convert.ToDouble(pieces[5]);
for (var evNum = 0; evNum < totalEvidences; evNum++)
{
var evidence = new Evidence
{
ObservedNet = target.AverageNet,
ObservedMonoisotopicMass = target.TheoreticalMonoIsotopicMass,
PredictedNet = target.PredictedNet,
NormalizedScore = normScore,
SeqWithNumericMods = target.EncodedNumericSequence,
Parent = target
};
target.Evidences.Add(evidence);
}
consensusTargets.Add(target.Id, target);
ctLine = ctReader.ReadLine();
}
while (protLine != null)
{
var pieces = protLine.Split(',');
var protein = new ProteinInformation
{
ProteinName = pieces[1]
};
proteins.Add(Convert.ToInt32(pieces[0]), protein);
protLine = protReader.ReadLine();
}
while (mapLine != null)
{
var pieces = mapLine.Split(',');
consensusTargets[Convert.ToInt32(pieces[0])].AddProtein(proteins[Convert.ToInt32(pieces[1])]);
mapLine = mapReader.ReadLine();
}
ctReader.Close();
protReader.Close();
mapReader.Close();
File.Delete(directory + "outTempAMT.txt");
File.Delete(directory + "outTempAMT_Proteins.txt");
File.Delete(directory + "outTempAMT_to_Protein_Map.txt");
var database = new TargetDatabase();
foreach (var target in consensusTargets)
{
database.AddConsensusTarget(target.Value);
}
database.Proteins = proteins.Values.ToList();
return(database);
}
/// <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 ComputeTerminusState(PeptideEvidence evidence, short numTrypticEnds, ProteinInformation protein)
{
if (evidence.Pre[0] == '-')
{
if (evidence.Post[0] == '-')
{
protein.TerminusState =
clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.ProteinNandCCTerminus;
protein.CleavageState = clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.Full;
}
else
{
protein.TerminusState = clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.ProteinNTerminus;
}
}
else if (evidence.Post[0] == '-')
{
protein.TerminusState = clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.ProteinCTerminus;
}
else
{
protein.TerminusState = clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.None;
}
switch (numTrypticEnds)
{
case 0:
protein.CleavageState = clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.NonSpecific;
break;
case 1:
protein.CleavageState =
clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.Partial;
break;
case 2:
protein.CleavageState = clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.Full;
break;
}
}
public ProteinTreeNodeViewModel(ProteinInformation protein, TreeNodeViewModel parent)
: base(String.Format("{0} ({1} peptides)", protein.ProteinName, protein.Consensus.Count), true, parent)
{
m_proteinInformation = protein;
}
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();
}
}
}
