CSMSL.Examples.ProteinGroupingExample.StartRamp C# (CSharp) Method

        public static void StartRamp(IProtease protease, double percentIdentifiedSteps = 0.05, int maxMissed = 3, int minLength = 5, int maxLength = 35)
        {
            List<Peptide> peps = new List<Peptide>();
            List<Protein> proteins = new List<Protein>();

            using (FastaReader reader = new FastaReader("Resources/yeast_uniprot_120226.fasta"))
            {
                foreach (Protein protein in reader.ReadNextProtein())
                {
                    foreach (Peptide peptide in protein.Digest(protease, maxMissed, minLength, maxLength))
                    {
                        peps.Add(peptide);
                    }
                    proteins.Add(protein);
                }
            }

            // Fixed seed to make it reproducible
            Random random = new Random(480912341);
            peps = peps.OrderBy(x => random.Next()).ToList();

            for (double percentIdentified = 0; percentIdentified <= 1; percentIdentified += percentIdentifiedSteps)
            {
                // Take the first x % to act as our identified peptides
                List<Peptide> identifiedPeptides = peps.Take((int) (peps.Count*percentIdentified)).ToList();

                List<ProteinGroup> proteinGroups = ProteinGroup.GroupProteins(proteins, protease, identifiedPeptides, new AminoAcidLeucineSequenceComparer(), maxMissed).ToList();
                Console.WriteLine("{0} peptides {1} protein groups", identifiedPeptides.Count, proteinGroups.Count);
            }
        }