//writes a list of proteins added to the exclusion list
private static void WriteExcludedProteinList(ExclusionProfile exclusionProfile)
{
List <string> excludedProteins = exclusionProfile.getDatabase().getExcludedProteins();
String outputFile = Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, "ExcludedProteinList.txt");
StreamWriter sw = new StreamWriter(outputFile);
foreach (String prot in excludedProteins)
{
sw.WriteLine(prot);
}
sw.Close();
}
private void postProcessingCalculations(int ddaNum, ProteinProphetResult ppr, ExclusionProfile exclusionProfile)
{
BaselineComparison bc = baselineComparisonSet[ddaNum];
List <String> proteinsIdentifiedByNoExclusion = bc.getProteinsIdentifiedByNoExclusion();
int totalResourcesNaiveExperiment = bc.getTotalResourcesNaiveExperiment();
int numProteinsIdentifiedNaiveExperiment = bc.getNumProteinsIdentifiedNaiveExperiment();
// set proteins identified first
setProteinsIdentified(ppr, proteinsIdentifiedByNoExclusion);
int correctlyExcluded = (int)data[Header.EvaluateExclusion_FoundOnCurrentExclusionList]
+ (int)data[Header.EvaluateExclusion_FoundOnCurrentObservedExclusionList];
int incorrectlyExcluded = (int)data[Header.EvaluateExclusion_NotFoundOnExclusionList];
/*
* found on past observed, found on past exclusion list, and found on future
* exclusion list are not incorrect exclusions, they are retention time being
* predicted incorrectly...
*/
double ratioIncorrectlyExcludedOverCorrectlyExcluded = takeRatio(incorrectlyExcluded, correctlyExcluded);
ChangeValue(Header.CorrectlyExcluded, correctlyExcluded);
ChangeValue(Header.IncorrectlyExcluded, incorrectlyExcluded);
ChangeValue(Header.RatioIncorrectlyExcludedOverCorrectlyExcluded, ratioIncorrectlyExcludedOverCorrectlyExcluded);
// Resources saved in total # available MS2 - # ms2 used foreach analysis
int resourcesSaved = totalResourcesNaiveExperiment - (int)data[Header.NumMS2Analyzed];
double percentResourcesSaved = takeRatio(resourcesSaved, totalResourcesNaiveExperiment);
double percentResourcesUsed = 1 - percentResourcesSaved;
ChangeValue(Header.PercentResourcesSaved, percentResourcesSaved);
ChangeValue(Header.PercentResourcesUsed, percentResourcesUsed);
/*-
* Protein Identification Sensitivity = # proteins identified / # proteins identified in whole experiment
* Protein Identification Fold Change = # proteins identified / # proteins identified by naive approach
* Protein Identification Sensitivity Limited DDA = # proteins identified also identified in naive approach / proteins identified by naive approach
*/
ChangeValue(Header.ProteinIdentificationSensitivity,
takeRatio((int)data[Header.NumProteinsIdentified], numProteinsIdentifiedOriginalExperiment));
ChangeValue(Header.ProteinIdentificationFoldChange,
takeRatio((int)data[Header.NumProteinsIdentified], numProteinsIdentifiedNaiveExperiment));
ChangeValue(Header.ProteinIdentificationSensitivityLimitedDDA,
takeRatio((int)data[Header.ProteinsIdentifiedInLimitedDDA], numProteinsIdentifiedNaiveExperiment));
List <String> inProgramExcludedProteins = exclusionProfile.getDatabase().getExcludedProteins();
int proteinOverlap_inProgramExcluded_vs_NoExclusion = compareProteins(inProgramExcludedProteins, proteinsIdentifiedByNoExclusion);
ChangeValue(Header.NumProteinOverlap_ExcludedProteinsAgainstNoExclusionProteins, proteinOverlap_inProgramExcluded_vs_NoExclusion);
ChangeValue(Header.ProteinGroupsIdentified, ppr.getFilteredProteinGroups().Count);
}
public static String DoJob(ProteinProphetResult ppr, ExclusionProfile exclusionProfile, int experimentNum)
{
String outputFile = Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, "NumberOfPeptidesPerIdentifiedProtein_" + experimentNum + ".txt");
StreamWriter sw = new StreamWriter(outputFile);
sw.WriteLine("Accession\tNumberOfPeptides\tSpectralCount");
List <String> confidentlyIdentifiedProts = ppr.getProteinsIdentified();
foreach (String accession in confidentlyIdentifiedProts)
{
Protein prot = exclusionProfile.getDatabase().getProtein(accession);
HashSet <String> peptidesObserved = new HashSet <String>();
foreach (PeptideScore pepEvidence in prot.getPeptideScore())
{
peptidesObserved.Add(pepEvidence.getPeptideSequence());
}
sw.WriteLine("{0}\t{1}\t{2}", accession, peptidesObserved.Count, prot.getPeptideScore().Count);
}
sw.Close();
return(outputFile);
}