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());
}
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());
}