private static void WriteGeneralAttributes(TextWriter writer, Transcript transcript)
{
var geneId = transcript.TranscriptSource == TranscriptDataSource.Ensembl
? transcript.Gene.EnsemblId.ToString()
: transcript.Gene.EntrezGeneId.ToString();
if (!string.IsNullOrEmpty(geneId))
{
writer.Write($"gene_id \"{geneId}\"; ");
}
if (!string.IsNullOrEmpty(transcript.Gene.Symbol))
{
writer.Write($"gene_name \"{transcript.Gene.Symbol}\"; ");
}
if (!transcript.Id.IsEmpty)
{
writer.Write($"transcript_id \"{FormatUtilities.CombineIdAndVersion(transcript.Id, transcript.Version)}\"; ");
}
writer.Write($"transcript_type \"{BioTypeUtilities.GetBiotypeDescription(transcript.BioType)}\"; ");
if (transcript.IsCanonical)
{
writer.Write("tag \"canonical\"; ");
}
if (!string.IsNullOrEmpty(transcript.Translation?.ProteinId.ToString()))
{
writer.Write($"protein_id \"{FormatUtilities.CombineIdAndVersion(transcript.Translation.ProteinId, transcript.Translation.ProteinVersion)}\"; ");
}
}
public void CombineIdAndVersion(string id, byte version, string expectedVersion)
{
var compactId = CompactId.Convert(id);
var observedVersion = FormatUtilities.CombineIdAndVersion(compactId, version);
Assert.Equal(expectedVersion, observedVersion);
}
/// <summary>
/// constructor
/// </summary>
public HgvsCodingNomenclature(TranscriptAnnotation ta, Transcript transcript, VariantFeature variant,
ICompressedSequence compressedSequence, bool isGenomicDuplicate)
{
_ta = ta;
_transcript = transcript;
_variant = variant;
_compressedSequence = compressedSequence;
_isGenomicDuplicate = isGenomicDuplicate;
_sb = new StringBuilder();
// get reference sequence strand
var transcriptOnReverseStrand = transcript.Gene.OnReverseStrand;
// this may be different to the input one for insertions/deletions
var altAllele = ta.AlternateAllele;
string variationFeatureSequence = altAllele.AlternateAllele;
// get the reverse complement of the vfs if needed
if (transcriptOnReverseStrand)
{
variationFeatureSequence = SequenceUtilities.GetReverseComplement(variationFeatureSequence);
}
// calculate the reference start and end
GetReferenceCoordinates(transcript, altAllele, out _hgvsStart, out _hgvsEnd);
// decide event type from HGVS nomenclature
_hgvsNotation = new HgvsNotation(ta.TranscriptReferenceAllele, variationFeatureSequence,
FormatUtilities.CombineIdAndVersion(transcript.Id, transcript.Version), _hgvsStart, _hgvsEnd,
_transcript.Translation != null);
}
public void CombineIdAndVersion()
{
const string expectedResult = "ENSG00000141510.7";
var id = CompactId.Convert("ENSG00000141510");
var observedResult = FormatUtilities.CombineIdAndVersion(id, 7);
Assert.Equal(expectedResult, observedResult);
}
internal static string GetProteinId(Transcript transcript)
{
var translation = transcript.Translation;
return(translation == null
? null
: FormatUtilities.CombineIdAndVersion(translation.ProteinId, translation.ProteinVersion));
}
/// <summary>
/// constructor
/// </summary>
public HgvsProteinNomenclature(VariantEffect variantEffect, TranscriptAnnotation ta, Transcript transcript,
VariantFeature variant, ICompressedSequence compressedSequence, AminoAcids aminoAcids)
{
_variantEffect = variantEffect;
_ta = ta;
_transcript = transcript;
_variant = variant;
_compressedSequence = compressedSequence;
_aminoAcids = aminoAcids;
_hgvsNotation = new HgvsNotation(_ta.ReferenceAminoAcids, _ta.AlternateAminoAcids,
FormatUtilities.CombineIdAndVersion(_transcript.Translation.ProteinId, _transcript.Translation.ProteinVersion),
_ta.ProteinBegin, _ta.ProteinEnd);
}
internal static string GetTranscriptId(Transcript transcript)
{
return(FormatUtilities.CombineIdAndVersion(transcript.Id, transcript.Version));
}