public static ProteinProphetResult RunProteinProphet(String cometFilePath, String outputFolder, Boolean keepResults)
{
Logger.debug("Post processing comet file: ");
Console.WriteLine("Runnign protein prophet, if program doesn't respond for a long time, try pressing a typing a few keys into the command line");
String proteinProphetOutput = ProteinProphetSearch(cometFilePath, outputFolder, keepResults);
ProteinProphetResult ppr = ProteinProphetEvaluator.getProteinProphetResult(proteinProphetOutput);
ppr.SetProteinGroup(ProteinProphetEvaluator.ExtractPositiveProteinGroups(proteinProphetOutput));
return(ppr);
}
/*
* Returns the ProteinProphetFile... this gives us a query-able object which can
* determine if a protein accession was identified by an experiment, as well as
* specific peptides.
*/
private static ProteinProphetFile processProteinProphetFile(String protXMLFileName)
{
const double fdr_threshold = 0.01; // 1% false discovery rate
double fdr = setFDRThreshold(protXMLFileName, fdr_threshold);
List <String> proteinGroupsData = extractProteinGroupsData(protXMLFileName);
List <String> filteredProteinsData = filterProteinsData(proteinGroupsData);
Dictionary <String, List <String> > proteinsToPeptides = extractPeptides(filteredProteinsData);
ProteinProphetFile ppf = new ProteinProphetFile(protXMLFileName, proteinsToPeptides, fdr,
protein_probablity_threshold);
ppf.getProteinProphetResult().SetProteinGroup(ProteinProphetEvaluator.ExtractPositiveProteinGroups(protXMLFileName));
return(ppf);
}