protected ProteinQuantificationEngineResult(ProteinGroup protein, List <Peptide> peptides, string controlCondition, string treatmentCondition)
{
this.Protein = protein;
this.Peptides = peptides;
this.ControlCondition = controlCondition;
this.TreatmentCondition = treatmentCondition;
}
public void WriteResults(string peaksOutputPath, string modPeptideOutputPath, string baseSeqPeptideOutputPath, string proteinOutputPath)
{
if (peaksOutputPath != null)
{
using (StreamWriter output = new StreamWriter(peaksOutputPath))
{
output.WriteLine(ChromatographicPeak.TabSeparatedHeader);
foreach (var peak in Peaks.SelectMany(p => p.Value))
{
output.WriteLine(peak.ToString());
}
}
}
if (modPeptideOutputPath != null)
{
using (StreamWriter output = new StreamWriter(modPeptideOutputPath))
{
output.WriteLine(Peptide.TabSeparatedHeader(SpectraFiles));
foreach (var peptide in PeptideModifiedSequences.OrderBy(p => p.Key))
{
output.WriteLine(peptide.Value.ToString(SpectraFiles));
}
}
}
if (baseSeqPeptideOutputPath != null)
{
using (StreamWriter output = new StreamWriter(baseSeqPeptideOutputPath))
{
output.WriteLine(Peptide.TabSeparatedHeader(SpectraFiles));
foreach (var peptide in PeptideBaseSequences.OrderBy(p => p.Key))
{
output.WriteLine(peptide.Value.ToString(SpectraFiles));
}
}
}
if (proteinOutputPath != null)
{
using (StreamWriter output = new StreamWriter(proteinOutputPath))
{
output.WriteLine(ProteinGroup.TabSeparatedHeader(SpectraFiles));
foreach (var protein in ProteinGroups.OrderBy(p => p.Key))
{
output.WriteLine(protein.Value.ToString(SpectraFiles));
}
}
}
}
public void MergeResultsWith(FlashLfqResults mergeFrom)
{
this.SpectraFiles.AddRange(mergeFrom.SpectraFiles);
foreach (var pep in mergeFrom.PeptideModifiedSequences)
{
if (this.PeptideModifiedSequences.TryGetValue(pep.Key, out var peptide))
{
Peptide mergeFromPep = pep.Value;
Peptide mergeToPep = peptide;
foreach (SpectraFileInfo file in mergeFrom.SpectraFiles)
{
mergeToPep.SetIntensity(file, mergeFromPep.GetIntensity(file));
mergeToPep.SetDetectionType(file, mergeFromPep.GetDetectionType(file));
}
}
else
{
this.PeptideModifiedSequences.Add(pep.Key, pep.Value);
}
}
foreach (var pg in mergeFrom.ProteinGroups)
{
if (this.ProteinGroups.TryGetValue(pg.Key, out var proteinGroup))
{
ProteinGroup mergeFromPg = pg.Value;
ProteinGroup mergeToPg = proteinGroup;
foreach (SpectraFileInfo file in mergeFrom.SpectraFiles)
{
mergeToPg.SetIntensity(file, mergeFromPg.GetIntensity(file));
}
}
else
{
this.ProteinGroups.Add(pg.Key, pg.Value);
}
}
foreach (var fromPeaks in mergeFrom.Peaks)
{
if (this.Peaks.TryGetValue(fromPeaks.Key, out var toPeaks))
{
toPeaks.AddRange(fromPeaks.Value);
}
else
{
this.Peaks.Add(fromPeaks.Key, fromPeaks.Value);
}
}
}
public void WriteResults(string peaksOutputPath, string modPeptideOutputPath, string proteinOutputPath, string bayesianProteinQuantOutput, bool silent)
{
if (!silent)
{
Console.WriteLine("Writing output...");
}
if (peaksOutputPath != null)
{
using (StreamWriter output = new StreamWriter(peaksOutputPath))
{
output.WriteLine(ChromatographicPeak.TabSeparatedHeader);
foreach (var peak in Peaks.SelectMany(p => p.Value)
.OrderBy(p => p.SpectraFileInfo.FilenameWithoutExtension)
.ThenByDescending(p => p.Intensity))
{
output.WriteLine(peak.ToString());
}
}
}
if (modPeptideOutputPath != null)
{
using (StreamWriter output = new StreamWriter(modPeptideOutputPath))
{
output.WriteLine(Peptide.TabSeparatedHeader(SpectraFiles));
foreach (var peptide in PeptideModifiedSequences.OrderBy(p => p.Key))
{
output.WriteLine(peptide.Value.ToString(SpectraFiles));
}
}
}
if (proteinOutputPath != null)
{
using (StreamWriter output = new StreamWriter(proteinOutputPath))
{
output.WriteLine(ProteinGroup.TabSeparatedHeader(SpectraFiles));
foreach (var protein in ProteinGroups.OrderBy(p => p.Key))
{
output.WriteLine(protein.Value.ToString(SpectraFiles));
}
}
}
if (bayesianProteinQuantOutput != null)
{
StringBuilder header = new StringBuilder();
StringBuilder[] proteinStringBuilders = new StringBuilder[ProteinGroups.Count];
for (int i = 0; i < proteinStringBuilders.Length; i++)
{
proteinStringBuilders[i] = new StringBuilder();
}
using (StreamWriter output = new StreamWriter(bayesianProteinQuantOutput))
{
if (!ProteinGroups.Any())
{
return;
}
var firstProteinQuantResults = ProteinGroups.First().Value.ConditionToQuantificationResults;
if (!firstProteinQuantResults.Any())
{
return;
}
string tabSepHeader = null;
if (firstProteinQuantResults.First().Value is PairedProteinQuantResult)
{
tabSepHeader = PairedProteinQuantResult.TabSeparatedHeader();
}
else
{
tabSepHeader = UnpairedProteinQuantResult.TabSeparatedHeader();
}
foreach (var condition in firstProteinQuantResults.Keys)
{
header.Append(tabSepHeader);
int p = 0;
// sort by protein false discovery rate, then by number of measurements
foreach (var protein in ProteinGroups
.OrderByDescending(v => v.Value.ConditionToQuantificationResults[condition].IsStatisticallyValid)
.ThenByDescending(v => v.Value.ConditionToQuantificationResults[condition].BayesFactor)
.ThenByDescending(v => v.Value.ConditionToQuantificationResults[condition].Peptides.Count))
{
proteinStringBuilders[p].Append(
protein.Value.ConditionToQuantificationResults[condition].ToString());
p++;
}
}
output.WriteLine(header);
foreach (var proteinStringBuilder in proteinStringBuilders)
{
output.WriteLine(proteinStringBuilder);
}
}
}
if (!silent)
{
Console.WriteLine("Finished writing output");
}
}
public void WriteResults(string peaksOutputPath, string modPeptideOutputPath, string proteinOutputPath, string bayesianProteinQuantOutput, bool silent)
{
if (!silent)
{
Console.WriteLine("Writing output...");
}
if (peaksOutputPath != null)
{
using (StreamWriter output = new StreamWriter(peaksOutputPath))
{
output.WriteLine(ChromatographicPeak.TabSeparatedHeader);
foreach (var peak in Peaks.SelectMany(p => p.Value))
{
output.WriteLine(peak.ToString());
}
}
}
if (modPeptideOutputPath != null)
{
using (StreamWriter output = new StreamWriter(modPeptideOutputPath))
{
output.WriteLine(Peptide.TabSeparatedHeader(SpectraFiles));
foreach (var peptide in PeptideModifiedSequences.OrderBy(p => p.Key))
{
output.WriteLine(peptide.Value.ToString(SpectraFiles));
}
}
}
if (proteinOutputPath != null)
{
using (StreamWriter output = new StreamWriter(proteinOutputPath))
{
output.WriteLine(ProteinGroup.TabSeparatedHeader(SpectraFiles));
foreach (var protein in ProteinGroups.OrderBy(p => p.Key))
{
output.WriteLine(protein.Value.ToString(SpectraFiles));
}
}
}
if (bayesianProteinQuantOutput != null)
{
StringBuilder header = new StringBuilder();
StringBuilder[] proteinStringBuilders = new StringBuilder[ProteinGroups.Count];
for (int i = 0; i < proteinStringBuilders.Length; i++)
{
proteinStringBuilders[i] = new StringBuilder();
}
using (StreamWriter output = new StreamWriter(bayesianProteinQuantOutput))
{
if (!ProteinGroups.Any())
{
return;
}
var firstProteinQuantResults = ProteinGroups.First().Value.ConditionToQuantificationResults;
if (!firstProteinQuantResults.Any())
{
return;
}
foreach (var condition in firstProteinQuantResults.Keys)
{
header.Append(ProteinQuantificationEngineResult.TabSeparatedHeader());
int p = 0;
// sort by protein false discovery rate, then by number of fold-change measurements
foreach (var protein in ProteinGroups
.OrderBy(v => v.Value.ConditionToQuantificationResults[condition].FalseDiscoveryRate)
.ThenByDescending(v => v.Value.ConditionToQuantificationResults[condition].PeptideFoldChangeMeasurements.SelectMany(b => b.foldChanges).Count()))
{
proteinStringBuilders[p].Append(
protein.Value.ConditionToQuantificationResults[condition].ToString());
p++;
}
}
output.WriteLine(header);
foreach (var proteinStringBuilder in proteinStringBuilders)
{
output.WriteLine(proteinStringBuilder);
}
}
}
if (!silent)
{
Console.WriteLine("Finished writing output");
}
}
private static void Main(string[] args)
{
Console.WriteLine("Welcome to MetaMorpheus");
// EDGAR: Createing the FlashLfqEngine is unforunately required,
// otherwise the code just crashes when executed.
SpectraFileInfo mzml = new SpectraFileInfo("sliced-mzml.mzml", "a", 0, 1, 0);
var pg = new FlashLFQ.ProteinGroup("MyProtein", "gene", "org");
Identification id3 = new Identification(mzml, "EGFQVADGPLYR", "EGFQVADGPLYR",
1350.65681, 94.12193, 2, new List <FlashLFQ.ProteinGroup> {
pg
});
Identification id4 = new Identification(mzml, "EGFQVADGPLYR", "EGFQVADGPLYR",
1350.65681, 94.05811, 2, new List <FlashLFQ.ProteinGroup> {
pg
});
FlashLfqEngine engine = new FlashLfqEngine(new List <Identification> {
id3, id4
}, normalize: true);
// EDGAR: End of part required to avoid crash
//generate toml
Console.WriteLine("generating toml with {0} key-value pairs", args[1]);
var tomlData = Toml.Create();
for (int i = 0; i < int.Parse(args[1]); i++)
{
tomlData.Add(i.ToString(), i);
}
//write toml
Console.WriteLine("writing toml file {0}", args[0]);
Stopwatch stopwatch = Stopwatch.StartNew();
Toml.WriteFile(tomlData, args[0]);
stopwatch.Stop();
Console.WriteLine("Time elapsed for toml write: {0}\n", stopwatch.ElapsedMilliseconds);
//read file
Console.WriteLine("reading toml file {0}", args[0]);
stopwatch = Stopwatch.StartNew();
var tomlRead = Toml.ReadFile(args[0]);
stopwatch.Stop();
Console.WriteLine("Time elapsed for toml read: {0}\n", stopwatch.ElapsedMilliseconds);
//read mzml file
Console.WriteLine("reading mzml file {0}", args[2]);
stopwatch = Stopwatch.StartNew();
var msData = Mzml.LoadAllStaticData(args[2]);
stopwatch.Stop();
Console.WriteLine("Time elapsed for mzML read: {0}\n", stopwatch.ElapsedMilliseconds);
//write mzml file
Console.WriteLine("writing mzml file {0}", args[3]);
stopwatch = Stopwatch.StartNew();
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(msData, args[3], false);
stopwatch.Stop();
Console.WriteLine("Time elapsed for mzML write: {0}", stopwatch.ElapsedMilliseconds);
}
