public override IEnumerable <string> Process()
{
//Extract chromotagraph information
var chroOptions = new ChromatographProfileBuilderOptions();
options.CopyProperties(chroOptions);
chroOptions.InputFile = options.InputFile;
chroOptions.OutputFile = options.BoundaryOutputFile;
chroOptions.DrawImage = false;
var builder = new ChromatographProfileBuilder(chroOptions);
if (!File.Exists(options.BoundaryOutputFile) || options.Overwrite)
{
Progress.SetMessage("Finding envelope ...");
builder.Progress = this.Progress;
builder.Process();
}
//Calculate deuterium enrichment for peptide
if (!File.Exists(options.DeuteriumOutputFile) || options.Overwrite)
{
Progress.SetMessage("Calculating deuterium ...");
var deuteriumOptions = new RTemplateProcessorOptions()
{
InputFile = options.BoundaryOutputFile,
OutputFile = options.DeuteriumOutputFile,
RTemplate = DeuteriumR,
RExecute = SystemUtils.GetRExecuteLocation(),
CreateNoWindow = true
};
deuteriumOptions.Parameters.Add("outputImage<-" + (options.DrawImage ? "1" : "0"));
deuteriumOptions.Parameters.Add("excludeIsotopic0<-" + (options.ExcludeIsotopic0 ? "1" : "0"));
new RTemplateProcessor(deuteriumOptions)
{
Progress = this.Progress
}.Process();
}
var deuteriumMap = new AnnotationFormat().ReadFromFile(options.DeuteriumOutputFile).ToDictionary(m => m.Annotations["ChroFile"].ToString());
//Read old spectra information
var format = new MascotPeptideTextFormat();
var spectra = format.ReadFromFile(options.InputFile);
foreach (var spec in spectra)
{
spec.Annotations.Remove("RetentionTime");
spec.Annotations.Remove("TheoreticalDeuterium");
spec.Annotations.Remove("ObservedDeuterium");
spec.Annotations.Remove("NumDeuteriumIncorporated");
spec.Annotations.Remove("NumExchangableHydrogen");
spec.Annotations.Remove("DeuteriumEnrichmentPercent");
}
var calcSpectra = new List <IIdentifiedSpectrum>();
var aas = new Aminoacids();
foreach (var pep in spectra)
{
var filename = Path.GetFileNameWithoutExtension(builder.GetTargetFile(pep));
if (deuteriumMap.ContainsKey(filename))
{
var numExchangeableHydrogens = aas.ExchangableHAtom(pep.Peptide.PureSequence);
var numDeuteriumIncorporated = double.Parse(deuteriumMap[filename].Annotations["NumDeuteriumIncorporated"] as string);
pep.Annotations["PeakRetentionTime"] = deuteriumMap[filename].Annotations["RetentionTime"];
pep.Annotations["TheoreticalDeuterium"] = deuteriumMap[filename].Annotations["TheoreticalDeuterium"];
pep.Annotations["ObservedDeuterium"] = deuteriumMap[filename].Annotations["ObservedDeuterium"];
pep.Annotations["NumDeuteriumIncorporated"] = deuteriumMap[filename].Annotations["NumDeuteriumIncorporated"];
pep.Annotations["NumExchangableHydrogen"] = numExchangeableHydrogens;
pep.Annotations["DeuteriumEnrichmentPercent"] = numDeuteriumIncorporated / numExchangeableHydrogens;
calcSpectra.Add(pep);
}
}
format.PeptideFormat.Headers = format.PeptideFormat.Headers + "\tPeakRetentionTime\tTheoreticalDeuterium\tObservedDeuterium\tNumDeuteriumIncorporated\tNumExchangableHydrogen\tDeuteriumEnrichmentPercent";
format.NotExportSummary = true;
format.WriteToFile(GetPeptideDeteriumFile(), calcSpectra);
var specGroup = calcSpectra.GroupBy(m => m.Peptide.PureSequence).OrderBy(l => l.Key).ToList();
var times = options.ExperimentalTimeMap.Values.Distinct().OrderBy(m => m).ToArray();
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("Peptide\t{0}", (from t in times select t.ToString()).Merge("\t"));
foreach (var peptide in specGroup)
{
var curSpectra = peptide.GroupBy(m => options.ExperimentalTimeMap[m.Query.FileScan.Experimental]).ToDictionary(l => l.Key, l => l.ToArray());
if (options.PeptideInAllTimePointOnly && times.Any(l => !curSpectra.ContainsKey(l)))
{
continue;
}
sw.Write(peptide.Key);
foreach (var time in times)
{
if (curSpectra.ContainsKey(time))
{
var deps = (from spec in curSpectra[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("Peptide deuterium enrichment calculation finished ...");
return(new string[] { options.OutputFile });
}
public override IEnumerable <string> Process()
{
var annos = new AnnotationFormat().ReadFromFile(boundaryFile);
var aas = new Aminoacids();
var pbuilder = new EmassProfileBuilder();
var chroFormat = new ChromatographProfileTextWriter();
foreach (var ann in annos)
{
var chroFile = Path.Combine(ann.Annotations["ChroDirectory"] as string, ann.Annotations["ChroFile"] as string) + ".tsv";
var peptide = (ann.Annotations["PeptideId"] as string).StringBefore("_");
var start = double.Parse(ann.Annotations["ChroLeft"] as string);
var end = double.Parse(ann.Annotations["ChroRight"] as string);
var chro = chroFormat.ReadFromFile(chroFile);
var chroFiltered = chro.Profiles.Where(l => l.RetentionTime >= start && l.RetentionTime <= end).ToArray();
//all observed isotopimers, start from 1, transfer to zero-based
var allIsotopics = (from f in chroFiltered
from s in f
select s.Isotopic - 1).Distinct().OrderBy(l => l).ToArray();
//get minimum intensity of each isotopimer
var minIntensities = (from iso in allIsotopics
select(from f in chroFiltered
where f.Count > iso
select f[iso].Intensity).Min()).ToArray();
//how many isotopic should I trust?
var iso0 = (from f in chroFiltered select f.First().Intensity).ToArray();
int maxIso = 1;
for (int i = 2; i < allIsotopics.Length; i++)
{
var isoi = (from f in chroFiltered select f.Count > i ? f[i].Intensity : minIntensities[i]).ToArray();
var corr = MathNet.Numerics.Statistics.Correlation.Pearson(iso0, isoi);
if (corr < minPearsonCorrelation)
{
maxIso = i;
break;
}
}
var maxIsoArray = allIsotopics.Where(l => l <= maxIso).ToArray();
//get observed profile in each scan
var observedIons = (from f in chroFiltered
select(from iso in maxIsoArray select f.Count > iso ? f[iso].Intensity : minIntensities[iso]).ToArray()).ToArray();
var atomComposition = aas.GetPeptideAtomComposition(peptide);
var hatom = (int)(Math.Round(aas.ExchangableHAtom(peptide)));
for (int h2 = 0; h2 < hatom; h2++)
{
}
var profiles = pbuilder.GetProfile(atomComposition, 1, 3);
var isotopicIons = (from peak in profiles
select new IsotopicIon()
{
Mz = peak.Mz,
Intensity = peak.Intensity,
}).ToArray();
}
return(null);
}
