private void LoadData()
{
try
{
Progress.SetMessage("Reading proteins from " + proteinFile + " ...");
format.Progress = Progress;
proteins = format.ReadFromFile(proteinFile);
List <IIdentifiedSpectrum> spectra = proteins.GetSpectra();
Progress.SetMessage("Reading itraqs from " + itrapFile + " ...");
ITraqItemUtils.LoadITraq(spectra, itrapFile, true, Progress);
for (int i = proteins.Count - 1; i >= 0; i--)
{
var group = proteins[i];
group[0].Peptides.RemoveAll(m => m.Spectrum.FindIsobaricItem() == null);
if (group[0].Peptides.Count == 0)
{
proteins.Remove(group);
}
}
}
catch (UserTerminatedException)
{
Progress.SetMessage("User terminated.");
}
catch (Exception ex)
{
Progress.SetMessage("Error : {0}", ex.Message);
MessageBox.Show(ex.Message);
}
}
protected List <IIdentifiedSpectrum> GetSpectra(string fileName)
{
Progress.SetMessage("Reading peptides ...");
List <IIdentifiedSpectrum> spectra = format.ReadFromFile(fileName);
Progress.SetMessage("Reading itraq ...");
IsobaricResult itraq = ITraqResultFileFormatFactory.GetXmlFormat().ReadFromFile(rawFileName);
Progress.SetMessage("Matching peptide and itraq ...");
ITraqItemUtils.MatchPeptideWithItraq(itraq, spectra);
return(spectra);
}
public override IEnumerable <string> Process(string fileName)
{
option.ProteinFileName = fileName;
Progress.SetMessage("Reading proteins...");
IIdentifiedResult ir = GetIdentifiedResult(fileName);
List <IIdentifiedSpectrum> spectra = ir.GetSpectra();
if (option.QuantifyModifiedPeptideOnly)
{
spectra.RemoveAll(m =>
{
foreach (char c in option.ModificationChars)
{
if (m.Sequence.Contains(c))
{
return(false);
}
}
return(true);
});
}
ITraqItemUtils.LoadITraq(spectra, option.ITraqFileName, false, this.Progress);
var itraqs = (from s in spectra
where s.FindIsobaricItem() != null
select s.FindIsobaricItem()).ToList();
if (itraqs.Count == 0)
{
throw new Exception("No itraq information matched from " + option.ITraqFileName);
}
Progress.SetMessage("Calculating ...");
var funcs = itraqs[0].PlexType.GetFuncs();
funcs.RemoveAll(m => option.References.Any(n => n.Name.Equals(m.Name)));
option.GetValidator().Validate(itraqs);
foreach (var dsName in option.DatasetMap.Keys)
{
var dsSet = new HashSet <string>(option.DatasetMap[dsName]);
foreach (var func in funcs)
{
var channelName = func.ChannelRatioName;
foreach (var group in ir)
{
CalculateProteinRatio(group, func.GetValue, dsName, channelName, dsSet);
}
}
}
if (option.NormalizeByMedianRatio)
{
foreach (var dsName in option.DatasetMap.Keys)
{
foreach (var func in funcs)
{
var channelName = func.ChannelRatioName;
var groups = (from g in ir
let item = g[0].FindITraqChannelItem(dsName, channelName)
where null != item && item.HasRatio
select new { Group = g, LogRatio = Math.Log(item.Ratio) }).ToList();
var ratios = (from g in groups
select g.LogRatio).ToArray();
if (ratios.Length > 1)
{
var mean = Statistics.Mean(ratios);
foreach (var g in groups)
{
var ratio = g.Group[0].FindITraqChannelItem(dsName, channelName).Ratio;
var logRatio = Math.Log(ratio);
var fixedLogRatio = logRatio - mean;
var fixedRatio = Math.Exp(fixedLogRatio);
foreach (var p in g.Group)
{
p.FindITraqChannelItem(dsName, channelName).Ratio = fixedRatio;
}
}
}
}
}
}
var irFormat = GetFormat(ir);
var refNames = (from refF in option.References
select refF.Name).Merge("");
string resultFileName = GetResultFileName(fileName, refNames);
irFormat.WriteToFile(resultFileName, ir);
string paramFileName = Path.ChangeExtension(resultFileName, ".param");
option.SaveToFile(paramFileName);
var statFileName = Path.ChangeExtension(resultFileName, ".stat");
using (StreamWriter sw = new StreamWriter(statFileName))
{
DoStatistic(sw, funcs, ir);
}
Progress.SetMessage("Finished.");
return(new[] { resultFileName, statFileName });
}
