Ejemplo n.º 1
0
        private static string Run()
        {
            StringBuilder sb = new StringBuilder();

            Sam    sam2a      = new Sam();
            string fileName2a = @"data\hw5-candidates-alpha.txt";
            string info2a     = sam2a.FindCandidates(fileName2a);

            sb.AppendLine("------------------");
            sb.AppendLine("Candidate Set 2a");
            sb.AppendLine("------------------");
            sb.AppendLine("File: " + fileName2a);
            sb.Append(info2a);
            sb.AppendLine();

            Meme meme2a = new Meme(sam2a, WMM.CreateWMM1());
            WMM  wmm2a  = meme2a.Run();

            List <MotifScan> motifScans0  = new List <MotifScan>();
            List <MotifScan> motifScans1  = new List <MotifScan>();
            List <MotifScan> motifScans2a = new List <MotifScan>();

            foreach (Read read in sam2a.Candidates)
            {
                MotifScan motifScan0 = new MotifScan("WMM0", WMM.CreateWMM0(), read);
                motifScan0.Scan();
                motifScans0.Add(motifScan0);

                MotifScan motifScan1 = new MotifScan("WMM1", WMM.CreateWMM1(), read);
                motifScan1.Scan();
                motifScans1.Add(motifScan1);

                MotifScan motifScan2a = new MotifScan("WMM2a", wmm2a, read);
                motifScan2a.Scan();
                motifScans2a.Add(motifScan2a);
            }

            sb.AppendLine("WMM0 Average Distance: " + CalculateAverageDistance(motifScans0));
            sb.AppendLine("WMM0 Relative Entropy: " + WMM.CreateWMM0().RelativeEntropy);
            sb.AppendLine("WMM0 Candidates with at least one hit: " + motifScans0.Count(ms => ms.TotalHitCount > 0));
            sb.AppendLine();
            sb.AppendLine("WMM1 Average Distance: " + CalculateAverageDistance(motifScans1));
            sb.AppendLine("WMM1 Relative Entropy: " + WMM.CreateWMM1().RelativeEntropy);
            sb.AppendLine("WMM1 Candidates with at least one hit: " + motifScans1.Count(ms => ms.TotalHitCount > 0));
            sb.AppendLine();
            sb.AppendLine("WMM2a Average Distance: " + CalculateAverageDistance(motifScans2a));
            sb.AppendLine("WMM2a Relative Entropy: " + wmm2a.RelativeEntropy);
            sb.AppendLine("WMM2a Candidates with at least one hit: " + motifScans2a.Count(ms => ms.TotalHitCount > 0));
            sb.AppendLine();


            // Filtered down, managable set of just the 0x4 matches
            Sam    sam2b      = new Sam();
            string fileName2b = @"C:\Users\jordanf\Downloads\SRR5831944.resorted2.sam";
            //string fileName2b = @"data\CandidateSuperset.sam";
            string info2b = sam2b.FindCandidates(fileName2b);

            sb.AppendLine();
            sb.AppendLine("------------------");
            sb.AppendLine("Candidate Set 2b");
            sb.AppendLine("------------------");
            sb.AppendLine("File: " + fileName2b);
            sb.Append(info2b);
            sb.AppendLine();

            Meme meme2b = new Meme(sam2b, WMM.CreateWMM1());
            WMM  wmm2b  = meme2b.Run();

            motifScans0 = new List <MotifScan>();
            motifScans1 = new List <MotifScan>();
            List <MotifScan> motifScans2b = new List <MotifScan>();

            foreach (Read read in sam2b.Candidates)
            {
                MotifScan motifScan0 = new MotifScan("WMM0", WMM.CreateWMM0(), read);
                motifScan0.Scan();
                motifScans0.Add(motifScan0);

                MotifScan motifScan1 = new MotifScan("WMM1", WMM.CreateWMM1(), read);
                motifScan1.Scan();
                motifScans1.Add(motifScan1);

                MotifScan motifScan2b = new MotifScan("WMM2b", wmm2b, read);
                motifScan2b.Scan();
                motifScans2b.Add(motifScan2b);
            }

            sb.AppendLine("WMM0 Average Distance: " + CalculateAverageDistance(motifScans0));
            sb.AppendLine("WMM0 Relative Entropy: " + WMM.CreateWMM0().RelativeEntropy);
            sb.AppendLine("WMM0 Candidates with at least one hit: " + motifScans0.Count(ms => ms.TotalHitCount > 0));
            sb.AppendLine();
            sb.AppendLine("WMM1 Average Distance: " + CalculateAverageDistance(motifScans1));
            sb.AppendLine("WMM1 Relative Entropy: " + WMM.CreateWMM1().RelativeEntropy);
            sb.AppendLine("WMM1 Candidates with at least one hit: " + motifScans1.Count(ms => ms.TotalHitCount > 0));
            sb.AppendLine();
            sb.AppendLine("WMM2b Average Distance: " + CalculateAverageDistance(motifScans2b));
            sb.AppendLine("WMM2b Relative Entropy: " + wmm2b.RelativeEntropy);
            sb.AppendLine("WMM2b Candidates with at least one hit: " + motifScans2b.Count(ms => ms.TotalHitCount > 0));

            PrintDistanceHistogram(motifScans0, "histogram0.csv");
            PrintDistanceHistogram(motifScans1, "histogram1.csv");
            PrintDistanceHistogram(motifScans2b, "histogram2b.csv");

            return(sb.ToString());
        }
Ejemplo n.º 2
0
        private static string Run2a()
        {
            StringBuilder sb = new StringBuilder();

            double secsToFindCandidates = 0;
            double secsToMotifScan      = 0;

            Stopwatch sw = new Stopwatch();

            sw.Start();

            Sam    sam  = new Sam();
            string info = sam.FindCandidates(@"data\hw5-candidates-alpha.txt");

            sb.AppendLine("------------------");
            sb.AppendLine("Info");
            sb.AppendLine("------------------");
            sb.Append(info);
            sb.AppendLine();

            secsToFindCandidates = sw.Elapsed.TotalSeconds;
            sw.Reset();

            Meme meme  = new Meme(sam, WMM.CreateWMM1());
            WMM  wmm2a = meme.Run();

            List <MotifScan> motifScans0  = new List <MotifScan>();
            List <MotifScan> motifScans1  = new List <MotifScan>();
            List <MotifScan> motifScans2a = new List <MotifScan>();

            foreach (Read read in sam.Candidates)
            {
                MotifScan motifScan0 = new MotifScan("WMM0", WMM.CreateWMM0(), read);
                motifScan0.Scan();
                motifScans0.Add(motifScan0);

                MotifScan motifScan1 = new MotifScan("WMM1", WMM.CreateWMM1(), read);
                motifScan1.Scan();
                motifScans1.Add(motifScan1);

                MotifScan motifScan2a = new MotifScan("WMM2a", wmm2a, read);
                motifScan2a.Scan();
                motifScans2a.Add(motifScan2a);
            }

            for (int i = 0; i < motifScans0.Count; i++)
            {
                sb.AppendLine("------------------");
                sb.AppendLine("Read Candidate: " + (i + 1));
                sb.AppendLine("------------------");
                sb.AppendLine(motifScans0[i].Print());
                sb.AppendLine(motifScans1[i].Print());
                sb.AppendLine(motifScans2a[i].Print());
            }

            sb.AppendLine();
            sb.AppendLine("------------------");
            sb.AppendLine("Summary");
            sb.AppendLine("------------------");
            sb.AppendLine();
            sb.AppendLine("WMM0 Average Distance: " + CalculateAverageDistance(motifScans0));
            sb.AppendLine("WMM0 Relative Entropy: " + WMM.CreateWMM0().RelativeEntropy);
            sb.AppendLine("WMM1 Average Distance: " + CalculateAverageDistance(motifScans1));
            sb.AppendLine("WMM1 Relative Entropy: " + WMM.CreateWMM1().RelativeEntropy);
            sb.AppendLine("WMM2a Average Distance: " + CalculateAverageDistance(motifScans2a));
            sb.AppendLine("WMM2a Relative Entropy: " + wmm2a.RelativeEntropy);

            secsToMotifScan = sw.Elapsed.TotalSeconds;
            sw.Stop();

            sb.AppendLine();
            sb.AppendFormat("FindCandidates took {0} seconds", secsToFindCandidates);
            sb.AppendLine();
            sb.AppendFormat("MotifScan took {0} seconds", secsToMotifScan);
            sb.AppendLine();

            return(sb.ToString());
        }