public void Should_return_proper_sequence()
{
const string expectedResult = "GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACA";
var result = _sut.Provide(".fasta", $"> Complement: Complement: HSBGPG Human gene for bone gla protein(BGP)\n{expectedResult}");
result.First().ToString().ShouldBe(expectedResult);
}
public IList <long> GetDeltas(SequenceModel[] sequenceData)
{
var sequences = sequenceData.Select(sequence => _provider.Provide(sequence?.FileName, sequence?.Content).First()).ToList();
_aligner = new DeltaAlignment(sequences.First(), sequences.Last());
return(_aligner.Deltas);
}
public IList <ISequenceAlignment> AlignSequences(SequenceModel[] sequenceData, int minimumScore = 200)
{
_aligner.MinimumScore = minimumScore;
var sequences = sequenceData.SelectMany(sequence => _provider.Provide(sequence?.FileName, sequence?.Content));
return(_aligner.Align(sequences));
}
public IEnumerable <Match> GetMatches(SequenceModel sequenceData)
{
var sequence = _sequenceProvider.Provide(sequenceData?.FileName, sequenceData?.Content)?.First();
_suffixTree = new MultiWaySuffixTree(sequence);
return(_suffixTree.SearchMatches(sequence));
}
public IDictionary <string, object> GetMetadata(SequenceModel[] sequenceData)
{
var sequences = sequenceData.SelectMany(sequence => _provider.Provide(sequence?.FileName, sequence?.Content)).ToList();
var alignment = new PairwiseSequenceAlignment(sequences.First(), sequences.Last());
return(alignment.Metadata);
}
public IDictionary <string, IList <int> > GetMatches(SequenceModel sequenceData, string[] searches, bool ignoreCase = false, int startIndex = 0)
{
var sequence = _sequenceProvider.Provide(sequenceData?.FileName, sequenceData?.Content)?.First();
_boyerMoore.IgnoreCase = ignoreCase;
_boyerMoore.StartIndex = startIndex;
return(_boyerMoore.FindMatch(sequence, searches));
}
public IndexModule(ISequenceProvider provider)
{
_provider = provider;
Get["/"] = parameters => View["index"];
Post["/Sequence/Parse"] = _ =>
{
var data = this.Bind <SequenceModel>();
return(Response.AsJson(_provider.Provide(data?.FileName, data?.Content).Select(x => x.ToString())));
};
}
private IEnumerable <TItem> BaseStatistics <TItem>(string fileName, string content,
Func <SequenceStatistics, TItem> selector)
{
var sequences = _sequenceProvider.Provide(fileName, content);
return(sequences.ToList().Select(x =>
{
var stats = new SequenceStatistics(x);
return selector(stats);
}));
}
public ISequence Translate(SequenceModel sequenceData)
{
var sequence = _provider.Provide(sequenceData?.FileName, sequenceData?.Content)?.First();
return(ProteinTranslation.Translate(sequence));
}
public IList <IPairwiseSequenceAlignment> AlignSequences(SequenceModel[] sequenceData)
{
var sequences = sequenceData.SelectMany(sequence => _provider.Provide(sequence?.FileName, sequence?.Content));
return(_aligner.Align(sequences));
}
public ISequence TranscribeToRNA(SequenceModel sequenceData)
{
var sequence = _sequenceProvider.Provide(sequenceData?.FileName, sequenceData?.Content)?.First();
return(Transcription.Transcribe(sequence));
}