private static void AssignCodonsAndAminoAcids(string transcriptRefAllele, string transcriptAltAllele,
IMappedPositions mappedPositions, ISequence codingSequence, AminoAcids aminoAcidProvier, out string refCodons,
out string altCodons, out string refAminoAcids, out string altAminoAcids)
{
AssignExtended(transcriptRefAllele, transcriptAltAllele, mappedPositions.CdsInterval,
mappedPositions.ProteinInterval, codingSequence, out refCodons, out altCodons);
aminoAcidProvier.Assign(refCodons, altCodons, out refAminoAcids, out altAminoAcids);
}
public PianoAnnotatedTranscript(ITranscript transcript, string referenceAminoAcids, string alternateAminoAcids, IMappedPositions mappedPositions, string upstreamAminoAcids,
string downStreamAminoAcids, IEnumerable <ConsequenceTag> consequences)
{
Transcript = transcript;
ReferenceAminoAcids = referenceAminoAcids;
AlternateAminoAcids = alternateAminoAcids;
MappedPositions = mappedPositions;
UpstreamAminoAcids = upstreamAminoAcids;
DownStreamAminoAcids = downStreamAminoAcids;
Consequences = consequences;
}
private static Tuple <string, string, string, string> GetCodonsAndAminoAcids(ITranscript transcript, ISequence refSequence,
string transcriptRefAllele, string transcriptAltAllele, ISimpleVariant variant,
IMappedPositions mappedPositions, AminoAcids aminoAcidsProvider)
{
var codingSequence = transcript.Translation == null
? null
: new CodingSequence(refSequence, transcript.Translation.CodingRegion.Start,
transcript.Translation.CodingRegion.End, transcript.CdnaMaps, transcript.Gene.OnReverseStrand,
transcript.StartExonPhase);
// compute codons and amino acids
AssignCodonsAndAminoAcids(transcriptRefAllele, transcriptAltAllele, mappedPositions,
codingSequence, aminoAcidsProvider, out string referenceCodons,
out string alternateCodons, out string referenceAminoAcids, out string alternateAminoAcids);
return(Tuple.Create(referenceCodons ?? "", alternateCodons ?? "", referenceAminoAcids ?? "",
alternateAminoAcids ?? ""));
}
private static VariantEffect GetVariantEffect(ITranscript transcript, ISimpleVariant variant, IMappedPositions mappedPositions, string refAminoAcids, string altAminoAcids, string refCodons, string altCodons, bool insertionInStartAndNoImpact)
{
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(transcript.Introns, variant, variant.Type);
positionalEffect.DetermineExonicEffect(transcript, variant, mappedPositions, variant.AltAllele, insertionInStartAndNoImpact);
var variantEffect = new VariantEffect(positionalEffect, variant, transcript, refAminoAcids,
altAminoAcids,
refCodons, altCodons, mappedPositions.ProteinInterval.Start);
return(variantEffect);
}