public override IEnumerable <string> Process()
{
var design = new IsobaricLabelingExperimentalDesign();
design.LoadFromFile(options.ExpermentalDesignFile);
string resultFileName = GetResultFilePrefix(options.ProteinFileName, design.GetReferenceNames(""));
string paramFileName = Path.ChangeExtension(resultFileName, ".param");
options.SaveToFile(paramFileName);
Progress.SetMessage("Reading proteins...");
IIdentifiedResult ir = new MascotResultTextFormat().ReadFromFile(options.ProteinFileName);
var proteinpeptidefile = string.Format("{0}.pro_pep.tsv", resultFileName);
using (var sw = new StreamWriter(proteinpeptidefile))
{
sw.WriteLine("Index\tPeptide\tProteins\tDescription\tPepCount\tUniquePepCount");
foreach (var g in ir)
{
var peps = g.GetPeptides();
var seqs = (from p in peps
select p.Peptide.PureSequence).Distinct().OrderBy(m => m).ToArray();
var proname = (from p in g select p.Name).Merge(" ! ");
var description = (from p in g select p.Description).Merge(" ! ");
foreach (var seq in seqs)
{
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}",
g.Index,
seq,
proname,
description,
g[0].PeptideCount,
g[0].UniquePeptideCount);
}
}
}
Progress.SetMessage("Quantifing proteins...");
var qoptions = new RTemplateProcessorOptions();
qoptions.InputFile = options.QuanPeptideFileName;
qoptions.OutputFile = resultFileName + ".quan." + options.PeptideToProteinMethod + ".tsv";
qoptions.RTemplate = string.Format("{0}/ProteinQuantification.r", FileUtils.GetTemplateDir(), options.PeptideToProteinMethod);
qoptions.Parameters.Add(string.Format("proteinfile<-\"{0}\"", proteinpeptidefile.Replace("\\", "/")));
qoptions.Parameters.Add(string.Format("method<-\"{0}\"", options.PeptideToProteinMethod));
qoptions.Parameters.Add("pvalue<-0.01");
qoptions.Parameters.Add("minFinalCount<-3");
new RTemplateProcessor(qoptions).Process();
Progress.SetMessage("Finished.");
return(new[] { qoptions.OutputFile });
}
protected virtual string GetResultFilePrefix(IsobaricLabelingExperimentalDesign design)
{
return(string.Format("{0}.{1}.{2}", options.PeptideFile, options.Mode, design.GetReferenceNames("")));
}