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 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");
}
}
