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>
/// Adds a target to the protein. If it already exists, the target is ignored.
/// </summary>
/// <param name="target"></param>
public void AddConsensusTarget(ConsensusTarget target)
{
if (!m_targets.ContainsKey(target.Id))
{
m_targets.Add(target.Id, target);
}
}
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);
}
public ConsensusTargetTreeNodeViewModel(ConsensusTarget ct, TreeNodeViewModel parent)
: base(String.Format("{0} ({1} evidences)", ct.EncodedNumericSequence, ct.Evidences.Count), true, parent)
{
m_consensusTarget = ct;
}
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>
/// Adds a target and its matching proteins to the database (unique)
/// </summary>
/// <param name="target"></param>
public void AddConsensusTarget(ConsensusTarget target)
{
ConsensusTargets.Add(target);
}
