public void Add(SpectrumSource ss)
{
byte[] msdataBytes = null;
if (ss.Metadata != null)
{
string tmpFilepath = Path.GetTempFileName() + ".mz5";
msdata.MSDataFile.write(ss.Metadata, tmpFilepath,
new msdata.MSDataFile.WriteConfig
{
format = MSDataFile.Format.Format_MZ5,
compression = MSDataFile.Compression.Compression_Zlib
});
msdataBytes = File.ReadAllBytes(tmpFilepath);
File.Delete(tmpFilepath);
}
insertRow(Table.SpectrumSource, new object[] { ss.Id, ss.Name, ss.URL, ss.Group.Id });
insertRow(Table.SpectrumSourceMetadata, new object[] { ss.Id, msdataBytes });
}
public IList <string> WriteIdpXml(bool includeScores, bool writeModFormula)
{
// get the set of distinct analysis/source pairs
var analysisSourcePairs = session.CreateQuery("SELECT psm.Analysis, psm.Spectrum.Source " +
"FROM PeptideSpectrumMatch psm " +
"GROUP BY psm.Analysis.id, psm.Spectrum.Source.id")
.List <object[]>();
// get the set of sources that have been in more than one analysis
var multiAnalyzedSources = session.CreateQuery("SELECT psm.Spectrum.Source.id " +
"FROM PeptideSpectrumMatch psm " +
"GROUP BY psm.Spectrum.Source.id " +
"HAVING COUNT(DISTINCT psm.Analysis.id) > 1")
.List <long>();
var outputPaths = new List <string>();
foreach (object[] analysisSourcePair in analysisSourcePairs)
{
Analysis a = analysisSourcePair[0] as Analysis;
SpectrumSource ss = analysisSourcePair[1] as SpectrumSource;
var settings = new XmlWriterSettings()
{
NewLineHandling = NewLineHandling.Replace,
NewLineChars = "\n",
Indent = true,
IndentChars = "\t"
};
string outputSuffix = ".idpXML";
if (multiAnalyzedSources.Contains(ss.Id.GetValueOrDefault()))
{
outputSuffix = "-" + a.Software.Name + "-" + a.StartTime.GetValueOrDefault().ToUniversalTime().ToString("yyyyMMddTHHmmss'Z'") + outputSuffix;
}
outputPaths.Add(ss.Name + outputSuffix);
var writer = XmlWriter.Create(outputPaths.Last(), settings);
writer.WriteStartDocument();
writer.WriteStartElement("idPickerPeptides");
#region <proteinIndex>
var proteinRows = session.CreateQuery("SELECT DISTINCT pro " +
"FROM Protein pro " +
"JOIN pro.Peptides pi " +
"JOIN pi.Peptide.Matches psm " +
"WHERE psm.Spectrum.Source.id = " + ss.Id)
.List <Protein>();
writer.WriteStartElement("proteinIndex");
writer.WriteAttribute("count", proteinRows.Count);
foreach (Protein pro in proteinRows)
{
writer.WriteStartElement("protein");
writer.WriteAttribute("id", pro.Id);
writer.WriteAttribute("locus", pro.Accession);
writer.WriteAttribute("decoy", 0);
writer.WriteAttribute("length", pro.Length);
writer.WriteAttribute("description", pro.Description);
writer.WriteEndElement();
}
writer.WriteEndElement(); // proteinIndex
#endregion
#region <peptideIndex>
var peptideRows = session.CreateQuery("SELECT DISTINCT psm.Peptide " +
"FROM PeptideSpectrumMatch psm " +
"WHERE psm.Spectrum.Source.id = " + ss.Id)
.List <Peptide>();
writer.WriteStartElement("peptideIndex");
writer.WriteAttribute("count", peptideRows.Count);
foreach (Peptide pep in peptideRows)
{
writer.WriteStartElement("peptide");
writer.WriteAttribute("id", pep.Id);
writer.WriteAttribute("sequence", pep.Sequence);
writer.WriteAttribute("mass", pep.MonoisotopicMass);
writer.WriteAttribute("unique", pep.Instances.Count > 1 ? 0 : 1);
writer.WriteAttribute("NTerminusIsSpecific", pep.Instances[0].NTerminusIsSpecific ? 1 : 0);
writer.WriteAttribute("CTerminusIsSpecific", pep.Instances[0].CTerminusIsSpecific ? 1 : 0);
foreach (PeptideInstance pi in pep.Instances)
{
writer.WriteStartElement("locus");
writer.WriteAttribute("id", pi.Protein.Id);
writer.WriteAttribute("offset", pi.Offset);
writer.WriteEndElement(); // locus
}
writer.WriteEndElement(); // peptide
}
writer.WriteEndElement(); // peptideIndex
#endregion
writer.WriteStartElement("spectraSources");
writer.WriteAttribute("count", 1);
{
writer.WriteStartElement("spectraSource");
writer.WriteAttribute("name", ss.Name);
writer.WriteAttribute("group", ss.Group.Name);
writer.WriteAttribute("count", ss.Spectra.Count);
{
#region <processingEventList>
writer.WriteStartElement("processingEventList");
writer.WriteAttribute("count", 2);
{
writer.WriteStartElement("processingEvent");
writer.WriteAttribute("type", "identification");
writer.WriteAttribute("start", a.StartTime.GetValueOrDefault().ToString("MM/dd/yyyy@HH:mm:ss"));
writer.WriteAttribute("end", a.StartTime.GetValueOrDefault().ToString("MM/dd/yyyy@HH:mm:ss")); // TODO: do we need end time?
writer.WriteAttribute("params", a.Parameters.Count);
if (a.Software != null)
{
a.Parameters.Add(new AnalysisParameter()
{
Name = "software name", Value = a.Software.Name
});
a.Parameters.Add(new AnalysisParameter()
{
Name = "software version", Value = a.Software.Version
});
}
foreach (AnalysisParameter ap in a.Parameters)
{
writer.WriteStartElement("processingParam");
writer.WriteAttribute("name", ap.Name);
writer.WriteAttribute("value", ap.Value);
writer.WriteEndElement(); // processingParam
}
if (a.Software != null)
{
a.Parameters.Remove(a.Parameters.Last());
a.Parameters.Remove(a.Parameters.Last());
}
writer.WriteEndElement(); // processingEvent
writer.WriteStartElement("processingEvent");
writer.WriteAttribute("type", "validation");
writer.WriteAttribute("start", DateTime.Now.ToString("MM/dd/yyyy@HH:mm:ss"));
writer.WriteAttribute("end", DateTime.Now.ToString("MM/dd/yyyy@HH:mm:ss"));
writer.WriteAttribute("params", a.Parameters.Count);
var validationParameters = new KeyValuePair <string, string>[]
{
new KeyValuePair <string, string>("software name", "IDPicker"),
new KeyValuePair <string, string>("software version", IDPicker.Util.Version),
new KeyValuePair <string, string>("MaxFDR", "1"),
};
foreach (var ap in validationParameters)
{
writer.WriteStartElement("processingParam");
writer.WriteAttribute("name", ap.Key);
writer.WriteAttribute("value", ap.Value);
writer.WriteEndElement(); // processingParam
}
writer.WriteEndElement(); // processingEvent
}
writer.WriteEndElement(); // processingEventList
#endregion
foreach (Spectrum s in ss.Spectra)
{
var psmList = s.Matches.Where(o => o.Analysis.Id == a.Id).OrderBy(o => o.Charge).ToList();
var distinctChargeStates = psmList.Select(o => o.Charge).Distinct();
// idpXML spectra are written per distinct charge state
foreach (int charge in distinctChargeStates)
{
var psmListAtCharge = psmList.Where(o => o.Charge == charge).ToList();
var distinctRanksAtCharge = psmListAtCharge.Select(o => o.Rank).OrderBy(o => o).Distinct();
#region <spectrum ...>
writer.WriteStartElement("spectrum");
writer.WriteAttribute("id", s.NativeID);
writer.WriteAttribute("index", s.Index);
writer.WriteAttribute("z", charge);
writer.WriteAttribute("mass", (s.PrecursorMZ * charge) - (pwiz.CLI.chemistry.Proton.Mass * charge));
// TODO: writer.WriteAttribute("time", s.ScanStartTime);
writer.WriteAttribute("results", distinctRanksAtCharge.Count());
// a result is a set of ids at a distinct rank
foreach (int rank in distinctRanksAtCharge)
{
var psmListAtRank = psmList.Where(o => o.Rank == rank).ToList();
writer.WriteStartElement("result");
writer.WriteAttribute("rank", rank);
writer.WriteAttribute("FDR", psmListAtRank[0].QValue);
writer.WriteAttribute("ids", psmListAtRank.Count);
if (includeScores)
{
string scores = String.Join(" ", psmListAtRank[0].Scores.Select(o => String.Format("{0}={1}", o.Key, o.Value)).ToArray());
writer.WriteAttribute("scores", scores);
}
foreach (PeptideSpectrumMatch psm in psmListAtRank)
{
writer.WriteStartElement("id");
writer.WriteAttribute("peptide", psm.Peptide.Id);
if (psm.Modifications.Count > 0)
{
var mods = new List <string>();
foreach (PeptideModification pm in psm.Modifications)
{
string offset;
switch (pm.Offset)
{
case int.MinValue: offset = "n"; break;
case int.MaxValue: offset = "c"; break;
default: offset = (pm.Offset + 1).ToString(); break;
}
mods.Add(String.Format("{0}:{1}", offset, writeModFormula ? pm.Modification.Formula : pm.Modification.MonoMassDelta.ToString()));
}
writer.WriteAttribute("mods", String.Join(" ", mods.ToArray()));
}
writer.WriteEndElement(); // id
}
writer.WriteEndElement(); // result
}
writer.WriteEndElement(); // spectrum
#endregion
}
}
}
writer.WriteEndElement(); // spectraSource
}
writer.WriteEndElement(); // spectraSources
writer.WriteEndDocument();
writer.Close();
}
return(outputPaths);
}
