public void TestPrepareOptions()
{
var options = new DeuteriumCalculatorOptions()
{
InputFile = "aaa",
};
Assert.IsFalse(options.PrepareOptions());
Assert.IsTrue(options.ParsingErrors.Any(l => l.Contains("aaa")));
}
protected override IProcessor GetProcessor()
{
var cm = pnlClassification.GetClassificationMap();
var expTimeMap = new Dictionary <string, double>();
foreach (var key in cm.Keys)
{
var keytime = double.Parse(key);
foreach (var v in cm[key])
{
expTimeMap[v] = keytime;
}
}
var options = new DeuteriumCalculatorOptions()
{
InputFile = noredundantFile.FullName,
OutputFile = noredundantFile.FullName + ".deuterium.tsv",
MinimumProfileLength = minimumProfileLength.Value,
MinimumIsotopicPercentage = minimumIsotopicPercentage.Value,
MinimumProfileCorrelation = minimumProfileCorrelation.Value,
MaximumProfileDistance = maximumProfileDistance.Value,
MzTolerancePPM = precursorPPMTolerance.Value,
Overwrite = cbOverwrite.Checked,
DrawImage = cbDrawImage.Checked,
ExcludeIsotopic0 = cbExcludeIsotopic0InFormula.Checked,
RawFiles = rawFiles.FileNames,
ThreadCount = threadCount.Value,
ExperimentalTimeMap = expTimeMap,
PeptideInAllTimePointOnly = rbPeptideInAllTimePointOnly.Checked
};
if (isPeptideFile(noredundantFile.FullName))
{
return(new PeptideDeuteriumCalculator(options));
}
else
{
return(new ProteinDeuteriumCalculator(options));
}
}
public override IEnumerable <string> Process()
{
//Prepare unique peptide file
var format = new MascotResultTextFormat();
var proteins = format.ReadFromFile(options.InputFile);
proteins.RemoveAmbiguousSpectra();
var spectra = proteins.GetSpectra();
foreach (var spec in spectra)
{
spec.Annotations.Remove("TheoreticalDeuterium");
spec.Annotations.Remove("ObservedDeuterium");
spec.Annotations.Remove("NumDeuteriumIncorporated");
spec.Annotations.Remove("NumExchangableHydrogen");
spec.Annotations.Remove("DeuteriumEnrichmentPercent");
}
var peptideFile = Path.ChangeExtension(options.InputFile, ".unique.peptides");
var peptideFormat = new MascotPeptideTextFormat(format.PeptideFormat.Headers);
peptideFormat.WriteToFile(peptideFile, spectra);
//Calculate deterium enrichment at peptide level
var pepOptions = new DeuteriumCalculatorOptions();
options.CopyProperties(pepOptions);
pepOptions.InputFile = peptideFile;
pepOptions.OutputFile = peptideFile + ".tsv";
var pepCalc = new PeptideDeuteriumCalculator(pepOptions);
pepCalc.Progress = this.Progress;
pepCalc.Process();
//Copy annotation from calculated peptide to original peptide
var calcSpectra = peptideFormat.ReadFromFile(pepCalc.GetPeptideDeteriumFile());
var oldSpectraMap = spectra.ToDictionary(m => m.Query.FileScan.LongFileName);
foreach (var calcSpec in calcSpectra)
{
var oldSpec = oldSpectraMap[calcSpec.Query.FileScan.LongFileName];
foreach (var ann in calcSpec.Annotations)
{
oldSpec.Annotations[ann.Key] = ann.Value;
}
}
//Remove the peptide not contain calculation result
for (int i = proteins.Count - 1; i >= 0; i--)
{
foreach (var protein in proteins[i])
{
protein.Peptides.RemoveAll(l => !l.Spectrum.Annotations.ContainsKey("DeuteriumEnrichmentPercent"));
}
if (proteins[i][0].Peptides.Count == 0)
{
proteins.RemoveAt(i);
}
}
format.PeptideFormat = peptideFormat.PeptideFormat;
var noredundantFile = Path.ChangeExtension(options.OutputFile, ".individual.tsv");
format.WriteToFile(noredundantFile, proteins);
var times = options.ExperimentalTimeMap.Values.Distinct().OrderBy(m => m).ToArray();
var timeFile = Path.ChangeExtension(options.OutputFile, ".times.tsv");
using (var sw = new StreamWriter(timeFile))
{
sw.WriteLine("Protein\t{0}", (from t in times select t.ToString()).Merge("\t"));
foreach (var protein in proteins)
{
var curSpectra = protein[0].GetSpectra();
if (options.PeptideInAllTimePointOnly)
{
var curMap = curSpectra.ToGroupDictionary(l => l.Peptide.PureSequence);
curSpectra.Clear();
foreach (var peps in curMap.Values)
{
var pepMap = peps.ToGroupDictionary(m => options.ExperimentalTimeMap[m.Query.FileScan.Experimental]);
if (times.All(time => pepMap.ContainsKey(time)))
{
curSpectra.AddRange(peps);
}
}
}
if (curSpectra.Count == 0)
{
continue;
}
sw.Write((from p in protein select p.Name).Merge("/"));
var curTimeMap = curSpectra.ToGroupDictionary(m => options.ExperimentalTimeMap[m.Query.FileScan.Experimental]);
foreach (var time in times)
{
if (curTimeMap.ContainsKey(time))
{
var deps = (from spec in curTimeMap[time] select double.Parse(spec.Annotations["DeuteriumEnrichmentPercent"].ToString())).ToArray();
var depMedian = Statistics.Median(deps);
sw.Write("\t{0:0.######}", depMedian);
}
else
{
sw.Write("\tNA");
}
}
sw.WriteLine();
}
}
Progress.SetMessage("Calculating ratio consistant ...");
var deuteriumOptions = new RTemplateProcessorOptions()
{
InputFile = timeFile,
OutputFile = options.OutputFile,
RTemplate = RatioR,
RExecute = SystemUtils.GetRExecuteLocation(),
CreateNoWindow = true
};
new RTemplateProcessor(deuteriumOptions)
{
Progress = this.Progress
}.Process();
Progress.SetMessage("Finished ...");
return(new string[] { options.OutputFile });
}
public PeptideDeuteriumCalculator(DeuteriumCalculatorOptions options)
{
this.options = options;
}
public ProteinDeuteriumCalculator(DeuteriumCalculatorOptions options)
{
this.options = options;
}