private void AddSuppIntervalToJsonObject(JsonObject jsonObject)
{
foreach (var si in SupplementaryIntervals)
{
jsonObject.AddObjectValue(si.JsonKey, si);
}
}
public void Annotate_RepeatExpansion_ExactMatch_OnePhenotype()
{
var variant = new RepeatExpansion(ChromosomeUtilities.Chr3, Start, End, "A", "<STR3>", null, 10, 5);
var annotatedPosition = GetAnnotatedPosition(variant);
_provider.Annotate(annotatedPosition);
var firstVariant = annotatedPosition.AnnotatedVariants[0];
Assert.NotNull(firstVariant.RepeatExpansionPhenotypes);
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddObjectValue(firstVariant.RepeatExpansionPhenotypes.JsonKey,
firstVariant.RepeatExpansionPhenotypes);
const string expectedJson = "\"repeatExpansionPhenotypes\":[{\"phenotype\":\"Spinocerebellar ataxia 7\",\"omimId\":164500,\"classifications\":[\"Normal\"],\"percentile\":6.33}]";
string observedJson = sb.ToString();
Assert.Equal(expectedJson, observedJson);
}
public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("transcript", Transcript.Id.WithVersion);
jsonObject.AddStringValue("source", Transcript.Source.ToString());
if (CompleteOverlap.HasValue && !CompleteOverlap.Value)
{
jsonObject.AddStringValue("bioType", GetBioType(Transcript.BioType));
}
jsonObject.AddStringValue("codons", GetCodonString(ReferenceCodons, AlternateCodons));
jsonObject.AddStringValue("aminoAcids", GetAminoAcidString(ReferenceAminoAcids, AlternateAminoAcids));
if (MappedPosition != null)
{
jsonObject.AddStringValue("cdnaPos", GetRangeString(MappedPosition.CoveredCdnaStart, MappedPosition.CoveredCdnaEnd));
jsonObject.AddStringValue("cdsPos", GetRangeString(MappedPosition.CoveredCdsStart, MappedPosition.CoveredCdsEnd));
jsonObject.AddStringValue("exons", GetFractionString(MappedPosition.ExonStart, MappedPosition.ExonEnd, Transcript.NumExons));
jsonObject.AddStringValue("introns", GetFractionString(MappedPosition.IntronStart, MappedPosition.IntronEnd, Transcript.NumExons - 1));
jsonObject.AddStringValue("proteinPos", GetRangeString(MappedPosition.CoveredProteinStart, MappedPosition.CoveredProteinEnd));
}
string geneId = Transcript.Source == Source.Ensembl
? Transcript.Gene.EnsemblId.ToString()
: Transcript.Gene.EntrezGeneId.ToString();
if (CompleteOverlap.HasValue && !CompleteOverlap.Value)
{
jsonObject.AddStringValue("geneId", geneId);
}
jsonObject.AddStringValue("hgnc", Transcript.Gene.Symbol);
if (Consequences != null)
{
AddConsequences(jsonObject);
}
jsonObject.AddStringValue("hgvsc", HgvsCoding);
jsonObject.AddStringValue("hgvsp", HgvsProtein);
jsonObject.AddObjectValue("geneFusion", _geneFusion);
jsonObject.AddBoolValue("isCanonical", Transcript.IsCanonical);
jsonObject.AddDoubleValue("polyPhenScore", PolyPhen?.Score);
jsonObject.AddStringValue("polyPhenPrediction", PolyPhen?.Prediction);
if (CompleteOverlap.HasValue && !CompleteOverlap.Value && Transcript.Translation != null)
{
jsonObject.AddStringValue("proteinId", Transcript.Translation.ProteinId.WithVersion);
}
jsonObject.AddDoubleValue("siftScore", Sift?.Score);
jsonObject.AddStringValue("siftPrediction", Sift?.Prediction);
if (ConservationScores != null && ConservationScores.Count > 0)
{
jsonObject.AddObjectValue("aminoAcidConservation", new AnnotatedConservationScore(ConservationScores));
}
if (CompleteOverlap.HasValue)
{
jsonObject.AddBoolValue("completeOverlap", CompleteOverlap.Value);
}
sb.Append(JsonObject.CloseBrace);
}