public async Task <string> SearchBlast(string seqString, CancellationToken cancellationToken)
{
NcbiBlastWebHandler handler = new NcbiBlastWebHandler()
{
LogOutput = Log,
EndPoint = "https://www.ncbi.nlm.nih.gov/blast/Blast.cgi",
TimeoutInSeconds = 3600
};
string cleanDNASequence = new string(seqString.Where(c => c == 'A' || c == 'G' || c == 'T' || c == 'C').ToArray());
Sequence sequence = new Sequence(DnaAlphabet.Instance, cleanDNASequence);
List <Bio.ISequence> sequences = new List <Bio.ISequence>();
sequences.Append(sequence);
var request = new BlastRequestParameters(sequences)
{
Database = "nt",
Program = BlastProgram.Blastn
};
request.Sequences.Add(sequence);
HttpContent result = handler.BuildRequest(request);
var executeResult = await handler.ExecuteAsync(request, cancellationToken);
if (executeResult == null)
{
return("Your sequence is not found (hits=0)");
}
//Stream stream = await result.ReadAsStreamAsync();
Bio.Web.Blast.BlastXmlParser parser = new BlastXmlParser();
var results = parser.Parse(executeResult).ToList();
var resString = String.Join(Environment.NewLine,
results.FirstOrDefault()
.Records.FirstOrDefault()
.Hits.Take(5)
.Select(x => $"ID: {x.Id}, Accession: {x.Accession}, Def: {x.Def}")
.ToArray());
return(resString);
}
/// <summary>
/// When implemented in a derived class and using the specified execution context, callback method, and user state, enqueues an asynchronous activity in a run-time workflow.
/// </summary>
/// <returns>
/// An object.
/// </returns>
/// <param name="context">Information that defines the execution environment for the <see cref="T:System.Activities.AsyncCodeActivity"/>.</param><param name="callback">The method to be called after the asynchronous activity and completion notification have occurred.</param><param name="state">An object that saves variable information for an instance of an asynchronous activity.</param>
protected override IAsyncResult BeginExecute(AsyncCodeActivityContext context, AsyncCallback callback, object state)
{
NcbiBlastWebHandler service = new NcbiBlastWebHandler();
// fill in the BLAST settings:
var searchParams = new BlastRequestParameters
{
Program = Program.Get(context) ?? DefaultProgram,
Database = Database.Get(context) ?? DefaultDatabase
};
searchParams.ExtraParameters.Add("Expect", "1e-10");
searchParams.Sequences.AddRange(Sequences.Get(context));
// Create the request
var runningTask = service.ExecuteAsync(searchParams, CancellationToken.None);
context.UserState = runningTask;
return(runningTask.AsApm(callback, state));
}
