public void WmmFullConsensusTest()
{
var wmmParameters = new FullConsensusWmm();
var wmmImpl = new WmmSequenceScanImpl(
wmmParameters,
sequence: "AAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGC",
scanLength: 6);
WmmSequenceResult result = wmmImpl.FindScoringSequences();
Assert.IsNotNull(result);
List <WmmSequenceResultItem> positiveScore = result.FoundSequences.Where(s => s.LogLikelihoodScore > 0).ToList();
}
public void WmmAlpha()
{
var wmmPartialParameters = new PartialConsensus();
var wmmFullParameters = new FullConsensusWmm();
string[] sequences = new[] {
"CTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAAC",
"CTCAAAAAAAAAAAAAAAAGATAATGGCTTCTTGAAAAAACAAAGAAATCAACCTGAAGGAATTCCTGATGGCCAAAGCTAGAACAATCTGAG",
"CGGTTTAAGAATACATCCTTGTATAATCTGACATACAAATTTGTCATTTCCTGCACATGCACACCATTGTTAAAAAAAAAAAAAAAAAGCCAG"
};
var wmmFullConsensesResults = new List <WmmSequenceResult>();
foreach (string sequence in sequences)
{
var wmmScan = new WmmSequenceScanImpl(
wmmFullParameters, sequence, scanLength: 6);
wmmFullConsensesResults.Add(wmmScan.FindScoringSequences());
}
Console.WriteLine("Enumerating Hits with LLR >0 for Full consensus");
var wmmFullConsensesResultItemFlattened = new List <WmmSequenceResultItem>();
var wmmFullConsensesResultItemFlattenedBestScoring = new List <WmmSequenceResultItem>();
foreach (WmmSequenceResult fullConsensusResult in wmmFullConsensesResults)
{
WmmSequenceResultItem bestScoring = null;
foreach (WmmSequenceResultItem item in fullConsensusResult.FoundSequences)
{
if (item.LogLikelihoodScore > 0)
{
wmmFullConsensesResultItemFlattened.Add(item);
if (bestScoring == null || bestScoring.LogLikelihoodScore <= item.LogLikelihoodScore)
{
bestScoring = item;
}
}
}
if (bestScoring != null)
{
wmmFullConsensesResultItemFlattenedBestScoring.Add(bestScoring);
}
}
Console.WriteLine("Total Count of hits: {0}", wmmFullConsensesResultItemFlattened.Count);
Console.WriteLine(
"Count of Sequences with hits: {0}", wmmFullConsensesResultItemFlattenedBestScoring.Count);
if (wmmFullConsensesResultItemFlattened.Count > 0)
{
Console.WriteLine(
"Average Distance to putative cleavage site {0}",
wmmFullConsensesResultItemFlattenedBestScoring.Average(b => b.DistanceFromCleavageSite));
}
Console.WriteLine("Wmm0");
Console.WriteLine(wmmFullParameters.Print());
Console.WriteLine("Relative Entropy :{0}", wmmFullParameters.GetRelativeEntropy());
var wmmPartialConsensesResults = new List <WmmSequenceResult>();
foreach (string sequence in sequences)
{
var wmmScan = new WmmSequenceScanImpl(
wmmPartialParameters, sequence, scanLength: 6);
wmmPartialConsensesResults.Add(wmmScan.FindScoringSequences());
}
Console.WriteLine("Enumerating Hits with LLR >0 for Partial consensus");
var wmmPartialConsensesResultItemFlattened = new List <WmmSequenceResultItem>();
var wmmPartialConsensesResultItemFlattenedBestScoring = new List <WmmSequenceResultItem>();
foreach (WmmSequenceResult partialConsensusResult in wmmPartialConsensesResults)
{
WmmSequenceResultItem bestScoring = null;
foreach (WmmSequenceResultItem item in partialConsensusResult.FoundSequences)
{
if (item.LogLikelihoodScore > 0)
{
wmmPartialConsensesResultItemFlattened.Add(item);
if (bestScoring == null || bestScoring.LogLikelihoodScore <= item.LogLikelihoodScore)
{
bestScoring = item;
}
}
}
if (bestScoring != null)
{
wmmPartialConsensesResultItemFlattenedBestScoring.Add(bestScoring);
}
}
Console.WriteLine("Total Count : {0}", wmmPartialConsensesResultItemFlattened.Count);
Console.WriteLine(
"Count of Sequences with hits: {0}", wmmPartialConsensesResultItemFlattenedBestScoring.Count);
if (wmmPartialConsensesResultItemFlattened.Count > 0)
{
Console.WriteLine(
"Average Distance to putative cleavage site {0}",
wmmPartialConsensesResultItemFlattenedBestScoring.Average(b => b.DistanceFromCleavageSite));
}
Console.WriteLine("Wmm1");
Console.WriteLine(wmmPartialParameters.Print());
Console.WriteLine("Relative Entropy :{0}", wmmPartialParameters.GetRelativeEntropy());
var wmmImpl = new MemeImpl(
wmmPartialParameters,
sequences: sequences,
scanLength: 6);
Dictionary <int, WmmSequenceResult> result = wmmImpl.FindScoringSequences(iterationCount: 1);
Console.WriteLine("Enumerating Hits with LLR >0 for Partial consensus");
var wmmPartialConsensesResultItemIteratedFlattened = new List <WmmSequenceResultItem>();
var wmmPartialConsensesResultItemIteratedFlattenedBestScoring = new List <WmmSequenceResultItem>();
foreach (var partialConsensusResult in result)
{
WmmSequenceResultItem bestScoring = null;
foreach (WmmSequenceResultItem item in partialConsensusResult.Value.FoundSequences)
{
if (item.LogLikelihoodScore > 0)
{
wmmPartialConsensesResultItemIteratedFlattened.Add(item);
if (bestScoring == null || bestScoring.LogLikelihoodScore <= item.LogLikelihoodScore)
{
bestScoring = item;
}
}
}
if (bestScoring != null)
{
wmmPartialConsensesResultItemIteratedFlattenedBestScoring.Add(bestScoring);
}
}
Console.WriteLine("Count : {0}", wmmPartialConsensesResultItemIteratedFlattened.Count);
Console.WriteLine(
"Count of Sequences with hits: {0}", wmmPartialConsensesResultItemIteratedFlattenedBestScoring.Count);
if (wmmPartialConsensesResultItemIteratedFlattened.Count > 0)
{
Console.WriteLine(
"Average Distance to putative cleavage site {0}",
wmmPartialConsensesResultItemIteratedFlattenedBestScoring.Average(b => b.DistanceFromCleavageSite));
}
Console.WriteLine("Wmm1");
Console.WriteLine(result[0].ParametersUsed.Print());
Console.WriteLine("Relative Entropy :{0}", result[0].ParametersUsed.GetRelativeEntropy());
Assert.IsNotNull(result);
}
public void WmmHumaGenome()
{
var wmmPartialParameters = new PartialConsensus();
var wmmFullParameters = new FullConsensusWmm();
var sequences = new List <string>();
using (StreamReader sr = File.OpenText(@"C:\temp\filtered_cleavagesite.txt"))
{
string s = String.Empty;
while ((s = sr.ReadLine()) != null)
{
sequences.Add(s.Split('\t')[1]);
}
};
var wmmFullConsensesResults = new List <WmmSequenceResult>();
foreach (string sequence in sequences)
{
var wmmScan = new WmmSequenceScanImpl(
wmmFullParameters, sequence, scanLength: 6);
wmmFullConsensesResults.Add(wmmScan.FindScoringSequences());
}
Console.WriteLine("Enumerating Hits with LLR >0 for Full consensus");
var wmmFullConsensesResultItemFlattened = new List <WmmSequenceResultItem>();
var wmmFullConsensesResultItemFlattenedBestScoring = new List <WmmSequenceResultItem>();
foreach (WmmSequenceResult fullConsensusResult in wmmFullConsensesResults)
{
WmmSequenceResultItem bestScoring = null;
foreach (WmmSequenceResultItem item in fullConsensusResult.FoundSequences)
{
if (item.LogLikelihoodScore > 0)
{
wmmFullConsensesResultItemFlattened.Add(item);
if (bestScoring == null || bestScoring.LogLikelihoodScore <= item.LogLikelihoodScore)
{
bestScoring = item;
}
}
}
if (bestScoring != null)
{
wmmFullConsensesResultItemFlattenedBestScoring.Add(bestScoring);
}
}
Console.WriteLine("Total Count of hits: {0}", wmmFullConsensesResultItemFlattened.Count);
Console.WriteLine(
"Count of Sequences with hits: {0}", wmmFullConsensesResultItemFlattenedBestScoring.Count);
if (wmmFullConsensesResultItemFlattened.Count > 0)
{
Console.WriteLine(
"Average Distance to putative cleavage site {0}",
wmmFullConsensesResultItemFlattenedBestScoring.Average(b => b.DistanceFromCleavageSite));
}
Console.WriteLine("Wmm0");
Console.WriteLine(wmmFullParameters.Print());
Console.WriteLine("Relative Entropy :{0}", wmmFullParameters.GetRelativeEntropy());
var wmmPartialConsensesResults = new List <WmmSequenceResult>();
foreach (string sequence in sequences)
{
var wmmScan = new WmmSequenceScanImpl(
wmmPartialParameters, sequence, scanLength: 6);
wmmPartialConsensesResults.Add(wmmScan.FindScoringSequences());
}
Console.WriteLine("Enumerating Hits with LLR >0 for Partial consensus");
var wmmPartialConsensesResultItemFlattened = new List <WmmSequenceResultItem>();
var wmmPartialConsensesResultItemFlattenedBestScoring = new List <WmmSequenceResultItem>();
foreach (WmmSequenceResult partialConsensusResult in wmmPartialConsensesResults)
{
WmmSequenceResultItem bestScoring = null;
foreach (WmmSequenceResultItem item in partialConsensusResult.FoundSequences)
{
if (item.LogLikelihoodScore > 0)
{
wmmPartialConsensesResultItemFlattened.Add(item);
if (bestScoring == null || bestScoring.LogLikelihoodScore <= item.LogLikelihoodScore)
{
bestScoring = item;
}
}
}
if (bestScoring != null)
{
wmmPartialConsensesResultItemFlattenedBestScoring.Add(bestScoring);
}
}
Console.WriteLine("Total Count : {0}", wmmPartialConsensesResultItemFlattened.Count);
Console.WriteLine(
"Count of Sequences with hits: {0}", wmmPartialConsensesResultItemFlattenedBestScoring.Count);
if (wmmPartialConsensesResultItemFlattened.Count > 0)
{
Console.WriteLine(
"Average Distance to putative cleavage site {0}",
wmmPartialConsensesResultItemFlattenedBestScoring.Average(b => b.DistanceFromCleavageSite));
}
Console.WriteLine("Wmm1");
Console.WriteLine(wmmPartialParameters.Print());
Console.WriteLine("Relative Entropy :{0}", wmmPartialParameters.GetRelativeEntropy());
var wmmImpl = new MemeImpl(
wmmPartialParameters,
sequences: sequences.ToArray(),
scanLength: 6);
Dictionary <int, WmmSequenceResult> result = wmmImpl.FindScoringSequences(iterationCount: 1);
Console.WriteLine("Enumerating Hits with LLR >0 for Partial consensus");
var wmmPartialConsensesResultItemIteratedFlattened = new List <WmmSequenceResultItem>();
var wmmPartialConsensesResultItemIteratedFlattenedBestScoring = new List <WmmSequenceResultItem>();
foreach (var partialConsensusResult in result)
{
WmmSequenceResultItem bestScoring = null;
foreach (WmmSequenceResultItem item in partialConsensusResult.Value.FoundSequences)
{
if (item.LogLikelihoodScore > 0)
{
wmmPartialConsensesResultItemIteratedFlattened.Add(item);
if (bestScoring == null || bestScoring.LogLikelihoodScore <= item.LogLikelihoodScore)
{
bestScoring = item;
}
}
}
if (bestScoring != null)
{
wmmPartialConsensesResultItemIteratedFlattenedBestScoring.Add(bestScoring);
}
}
Console.WriteLine("Count : {0}", wmmPartialConsensesResultItemIteratedFlattened.Count);
Console.WriteLine(
"Count of Sequences with hits: {0}", wmmPartialConsensesResultItemIteratedFlattenedBestScoring.Count);
if (wmmPartialConsensesResultItemIteratedFlattened.Count > 0)
{
Console.WriteLine(
"Average Distance to putative cleavage site {0}",
wmmPartialConsensesResultItemIteratedFlattenedBestScoring.Average(b => b.DistanceFromCleavageSite));
}
Console.WriteLine("Wmm1");
Console.WriteLine(result[0].ParametersUsed.Print());
Console.WriteLine("Relative Entropy :{0}", result[0].ParametersUsed.GetRelativeEntropy());
Assert.IsNotNull(result);
}
