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 });
}
private void AssignFromOption(IsobaricLabelingExperimentalDesign option)
{
iTraqFile.FullName = option.IsobaricFile;
refChannels.SelectedIons = (from f in option.References
select f.Name).Merge(",");
pnlClassification.SetClassificationSet(option.DatasetMap);
}
protected IsobaricLabelingExperimentalDesign GetStatisticOption()
{
var option = new IsobaricLabelingExperimentalDesign();
option.DatasetMap = pnlClassification.GetClassificationSet();
option.IsobaricFile = iTraqFile.FullName;
option.References = GetReferenceFuncs();
option.PlexType = IsobaricScanXmlUtils.GetIsobaricType(txtIsobaricXmlFile.Text);
return(option);
}
private void btnCancel_Click(object sender, EventArgs e)
{
var dlg = loadArgument.GetFileDialog();
if (dlg.ShowDialog(this) == DialogResult.OK)
{
IsobaricLabelingExperimentalDesign option = new IsobaricLabelingExperimentalDesign();
try
{
option.LoadFromFile(dlg.FileName);
AssignFromOption(option);
}
catch (Exception ex)
{
MessageBox.Show(this, ex.Message, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
}
public override IEnumerable <string> Process()
{
var design = new IsobaricLabelingExperimentalDesign();
design.LoadFromFile(options.DesignFile);
string resultFileName = GetResultFilePrefix(design);
string paramFileName = Path.ChangeExtension(resultFileName, ".param");
options.SaveToFile(paramFileName);
Progress.SetMessage("Reading peptides...");
List <IIdentifiedSpectrum> spectra = new MascotPeptideTextFormat().ReadFromFile(options.PeptideFile);
IsobaricScanUtils.Load(spectra, design.IsobaricFile, false, this.Progress);
var isoSpectra = (from s in spectra
where s.FindIsobaricItem() != null
select s).ToList();
if (isoSpectra.Count == 0)
{
throw new Exception(string.Format("No isobaric labelling information between {0} and {1}", options.PeptideFile, options.DesignFile));
}
if (options.PerformNormalizition)
{
var msg = "Normalizing channels using loess algorithm";
var detailsDir = resultFileName + ".details";
if (!Directory.Exists(detailsDir))
{
Directory.CreateDirectory(detailsDir);
}
var isoGroup = isoSpectra.GroupBy(m => m.Query.FileScan.Experimental).ToList();
Progress.SetRange(0, isoGroup.Count);
Progress.SetPosition(0);
var fileIndex = 0;
foreach (var isoFile in isoGroup)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
fileIndex++;
Progress.SetMessage("{0} {1}/{2} ...", msg, fileIndex, isoGroup.Count);
var datafile = string.Format("{0}\\{1}.{2}.tsv", detailsDir, Path.GetFileNameWithoutExtension(resultFileName), isoFile.Key);
var rresultfile = Path.ChangeExtension(datafile, ".norm.tsv");
//if (!File.Exists(rresultfile))
{
using (var sw = new StreamWriter(datafile))
{
sw.WriteLine("FileScan\t{0}", (from cha in design.PlexType.Channels select cha.Name).Merge("\t"));
foreach (var isoSpec in isoFile)
{
sw.Write("{0}", isoSpec.Query.FileScan.LongFileName);
var item = isoSpec.FindIsobaricItem();
for (int i = 0; i < design.PlexType.Channels.Count; i++)
{
sw.Write("\t{0:0.0}", item[i].Intensity);
}
sw.WriteLine();
}
}
var roptions = new RTemplateProcessorOptions();
roptions.InputFile = datafile;
roptions.OutputFile = rresultfile;
roptions.Parameters.Add(string.Format("missingvalue<-{0}", IsobaricConsts.NULL_INTENSITY));
roptions.RTemplate = FileUtils.GetTemplateDir() + "/CyclicLoessNormalization.r";
new RTemplateProcessor(roptions).Process();
Progress.SetPosition(fileIndex);
}
var specMap = isoFile.ToDictionary(m => m.Query.FileScan.LongFileName);
//read R result to replace the intensity of each spectrum
using (var sr = new StreamReader(rresultfile))
{
//ignore header
string line = sr.ReadLine();
IIdentifiedSpectrum spec;
while ((line = sr.ReadLine()) != null)
{
if (string.IsNullOrWhiteSpace(line))
{
break;
}
var parts = line.Split('\t');
if (!specMap.TryGetValue(parts[0], out spec))
{
throw new Exception(string.Format("{0} can not be found! The first column of normalization result file {1} must be FileScan!", parts[0], rresultfile));
}
var item = spec.FindIsobaricItem();
for (int i = 1; i < parts.Length; i++)
{
item[i - 1].Intensity = double.Parse(parts[i]);
}
}
}
}
}
Progress.SetMessage("Quantifying peptide with outlier detection ...");
FilterSpectraByQuantifyMode(isoSpectra);
var refFuncs = design.References;
var samFuncs = design.GetSamples();
var pepfile = resultFileName + ".tsv";
using (var sw = new StreamWriter(pepfile))
{
sw.WriteLine("Subject\tDataset\tFileScan\tSequence\tREF\t{0}",
samFuncs.ConvertAll(m => m.Name).Merge("\t"));
Func <IIdentifiedSpectrum, string> keyFunc;
if (options.Mode == QuantifyMode.qmModificationSite)
{
keyFunc = m => m.GetMatchSequence();
}
else
{
keyFunc = m => m.Peptide.PureSequence;
}
var peptides = isoSpectra.ToGroupDictionary(m => keyFunc(m)).OrderBy(m => m.Key).ToList();
foreach (var pep in peptides)
{
foreach (var dsName in design.DatasetMap.Keys)
{
var dsSet = new HashSet <string>(design.DatasetMap[dsName]);
var dsSpectra = (from s in pep.Value
where dsSet.Contains(s.Query.FileScan.Experimental)
orderby s.Peptide.Sequence
select s).ToList();
foreach (var spec in dsSpectra)
{
var isoitem = spec.FindIsobaricItem();
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4:0.0}\t{5}",
pep.Key,
dsName,
spec.Query.FileScan.ShortFileName,
spec.Peptide.Sequence,
refFuncs.ConvertAll(m => m.GetValue(isoitem)).Sum(),
samFuncs.ConvertAll(m => string.Format("{0:0.0}", m.GetValue(isoitem))).Merge("\t"));
}
}
}
}
var qoptions = new RTemplateProcessorOptions();
qoptions.InputFile = pepfile;
qoptions.OutputFile = resultFileName + ".quan.tsv";
qoptions.RTemplate = string.Format("{0}/PeptideQuantification.r", FileUtils.GetTemplateDir());
qoptions.Parameters.Add(string.Format("missingvalue<-{0}", IsobaricConsts.NULL_INTENSITY));
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("")));
}
