internal static ProteinChange GetProteinChange(int start, string refAminoAcids, string altAminoAcids,
string peptideSeq, IVariantEffect variantEffect)
{
if (refAminoAcids == altAminoAcids ||
variantEffect.IsStopRetained())
{
return(ProteinChange.None);
}
//insertion before the transcript
if (refAminoAcids.Length == 0 && start == 1)
{
return(ProteinChange.None);
}
if (variantEffect.IsStartLost())
{
return(ProteinChange.StartLost);
}
// todo: add start gained
// according to var nom, only if the Stop codon is effected, we call it an extension
if (variantEffect.IsStopLost() && refAminoAcids.StartsWith(AminoAcids.StopCodon))
{
return(ProteinChange.Extension);
}
if (variantEffect.IsFrameshiftVariant())
{
return(ProteinChange.Frameshift);
}
if (altAminoAcids.Length > refAminoAcids.Length && HgvsUtilities.IsAminoAcidDuplicate(start, altAminoAcids, peptideSeq))
{
return(ProteinChange.Duplication);
}
if (refAminoAcids.Length == 0 && altAminoAcids.Length != 0)
{
return(ProteinChange.Insertion);
}
if (refAminoAcids.Length != 0 && altAminoAcids.Length == 0)
{
return(ProteinChange.Deletion);
}
if (refAminoAcids.Length == 1 && altAminoAcids.Length == 1)
{
return(ProteinChange.Substitution);
}
// the only remaining possibility is deletions/insertions
return(ProteinChange.DelIns);
}
private static List <ConsequenceTag> GetConsequences(IInterval transcript, IVariant variant,
IVariantEffect variantEffect)
{
var featureEffect = new FeatureVariantEffects(transcript, variant.Type, variant,
variant.IsStructuralVariant);
var consequence = new Consequences(variantEffect, featureEffect);
consequence.DetermineSmallVariantEffects();
return(consequence.GetConsequences());
}
private static List <ConsequenceTag> GetConsequences(IInterval transcript, bool onReverseStrand, IVariant variant,
IVariantEffect variantEffect)
{
OverlapType overlapType = Intervals.Utilities.GetOverlapType(transcript.Start, transcript.End, variant.Start, variant.End);
EndpointOverlapType endpointOverlapType = Intervals.Utilities.GetEndpointOverlapType(transcript.Start, transcript.End, variant.Start, variant.End);
var featureEffect = new FeatureVariantEffects(overlapType, endpointOverlapType, onReverseStrand, variant.Type, variant.IsStructuralVariant);
var consequence = new Consequences(variant.Type, variantEffect, featureEffect);
consequence.DetermineSmallVariantEffects();
return(consequence.GetConsequences());
}
public Consequences(IVariantEffect variantEffect = null, IFeatureVariantEffects featureEffect = null)
{
_consequences = new List <ConsequenceTag>();
_variantEffect = variantEffect;
_featureEffect = featureEffect;
}