/**
* TODO: Avec frequency > 2 pour les autres Alternatives ? Inutile pour l'instant
*/
public async Task <FrequencyReport> SnpFrequency(string referenceId, Snp snp, int windowSize = 20,
int validateSize = 5)
{
var genome = await Reader.ReadSequenceAsync(referenceId);
if (genome[snp.Position0].ToString() != snp.Reference)
{
throw new Exception("Reference mismatch");
}
var beforeWindow = new Range(snp.Position0 - windowSize, snp.Position0);
var afterWindow = new Range(snp.Position0 + 1, snp.Position0 + 1 + windowSize);
var seq1 = genome[beforeWindow] + genome[snp.Position0] + genome[afterWindow];
var seq2 = genome[beforeWindow] + snp.Insertion + genome[afterWindow];
var options = await BlastnOptions.FromInlineQuery($">id\n{seq2}");
options.Evalue = "1e-5";
options.Task = "blastn";
options.MaxTargetSeqs = 150;
options.FormatSpecifiers = new List <string> {
"sseq"
};
var results = await Client.ExecuteBuffered(options);
var validateBefore = new Range(windowSize - validateSize + 1, windowSize + 1);
var validateAfter = new Range(windowSize, windowSize + validateSize);
var frequencies = new FrequencyReport(2);
foreach (var result in results)
{
if (String.IsNullOrEmpty(result.AlignedPartOfSubjectSequence))
{
continue;
}
if (result.AlignedPartOfSubjectSequence.Contains(seq1[validateBefore]))
{
frequencies.Increment(0);
}
if (result.AlignedPartOfSubjectSequence.Contains(seq1[validateAfter]))
{
frequencies.Increment(0);
}
if (result.AlignedPartOfSubjectSequence.Contains(seq2[validateBefore]))
{
frequencies.Increment(1);
}
if (result.AlignedPartOfSubjectSequence.Contains(seq2[validateAfter]))
{
frequencies.Increment(1);
}
}
return(frequencies);
}
public async Task <List <BlastnResult> > ExecuteBuffered(BlastnOptions options)
{
var env = options.GetEnv();
env["BLASTDB"] = DbPath;
var args = options.GetArguments();
args.Add($"-db {DbName}");
var command = Cli
.Wrap(BlastnPath)
.WithArguments(args, false)
.WithEnvironmentVariables(env);
var result = await command.ExecuteBufferedAsync();
var blastnResults = result.StandardOutput.Split('\n')
.Where(v => !string.IsNullOrEmpty(v))
.Select(v => BlastnResult.FromOutput(options, v))
.ToList();
return(blastnResults);
}
