public BaselineComparison(ProteinProphetResult ppr, int numMS2, int ddaNum)
{
proteinsIdentifiedByNoExclusion = ppr.getProteinsIdentified();
numProteinsIdentifiedNaiveExperiment = proteinsIdentifiedByNoExclusion.Count;
totalResourcesNaiveExperiment = numMS2;
this.ddaNum = ddaNum;
}
private void setProteinsIdentified(ProteinProphetResult ppr, List <String> proteinsIdentifiedByNoExclusion)
{
if (ppr != null)
{
List <String> proteinsIdentified = ppr.getProteinsIdentified();
int intersect = compareProteins(proteinsIdentifiedByNoExclusion, proteinsIdentified);
ChangeValue(Header.NumProteinsIdentified, proteinsIdentified.Count);
ChangeValue(Header.ProteinsIdentifiedInLimitedDDA, intersect);
}
}
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);
}
public static void DoJob()
{
StreamWriter sw = new StreamWriter(Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, "ExcludedProteinComparison.txt"));
String ExcludedProteinFile = "C:\\Coding\\2019LavalleeLab\\temp2\\Output\\Gold_MLGE_nonCheat.txt_output\\ExcludedProteinList.txt";
StreamReader sr = new StreamReader(ExcludedProteinFile);
List <String> inProgramConfidentlyIdentified = new List <String>();
String line = sr.ReadLine();
while (line != null)
{
inProgramConfidentlyIdentified.Add(line);
line = sr.ReadLine();
}
String proteinProphetFile = "C:\\Coding\\2019LavalleeLab\\GitProjectRealTimeMS\\TestData\\PreComputedFiles\\MS_QC_120min_interact.prot.xml";
ProteinProphetResult ppr = ProteinProphetEvaluator.getProteinProphetResult(proteinProphetFile);
List <String> realConfidentIdentified = ppr.getProteinsIdentified();
List <String> intersection = ListUtil.FindIntersection(inProgramConfidentlyIdentified, realConfidentIdentified);
sw.WriteLine("In-Program excluded: {0}", inProgramConfidentlyIdentified.Count);
sw.WriteLine("Real confidently identified: {0}", realConfidentIdentified.Count);
sw.WriteLine("Intersection: {0}", intersection.Count);
sw.Close();
}