public override IEnumerable <string> Process(string fileName)
{
Progress.SetMessage("Reading mutation file ...");
var format = new MascotPeptideTextFormat();
var spectra = format.ReadFromFile(fileName);
var quanFormat = new MascotResultTextFormat();
quanFormat.Progress = this.Progress;
Progress.SetMessage("Reading quantification file ...");
var ir = quanFormat.ReadFromFile(quantificationFile);
if (ir.Count == 0)
{
throw new Exception("No quantification found!");
}
foreach (var pep in spectra)
{
var mutSeq = pep.Peptide.PureSequence.Replace('I', 'L');
var mutProtein = ir.FirstOrDefault(m => m.Any(n => n.Name.Equals(mutSeq)));
if (mutProtein != null)
{
AddRatio(pep, mutProtein, "MUL_");
}
var oriSeq = pep.Annotations["OriginalSequence"] as string;
var oriProtein = ir.FirstOrDefault(m => m.Any(n => n.Name.Equals(oriSeq)));
if (oriProtein != null)
{
AddRatio(pep, oriProtein, "ORI_");
}
}
format.Initialize(spectra);
var result = fileName + ".quantification";
Progress.SetMessage("Writing peptide quantification file ...");
format.WriteToFile(result, spectra);
return(new string[] { result });
}
