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);
}
/// <summary>
/// populates the consequences list with tier 3 consequences if found (NOTE: Tests are done in rank order)
/// </summary>
private void GetTier3Types()
{
// SpliceDonorVariant
if (_variantEffect.IsSpliceDonorVariant())
{
_consequences.Add(ConsequenceTag.splice_donor_variant);
}
// SpliceAcceptorVariant
if (_variantEffect.IsSpliceAcceptorVariant())
{
_consequences.Add(ConsequenceTag.splice_acceptor_variant);
}
// StopGained
if (_variantEffect.IsStopGained())
{
_consequences.Add(ConsequenceTag.stop_gained);
}
// FrameshiftVariant
if (_variantEffect.IsFrameshiftVariant())
{
_consequences.Add(ConsequenceTag.frameshift_variant);
}
// StopLost
if (_variantEffect.IsStopLost())
{
_consequences.Add(ConsequenceTag.stop_lost);
}
if (_variantEffect.IsStartLost())
{
_consequences.Add(ConsequenceTag.start_lost);
}
// InframeInsertion
if (_variantEffect.IsInframeInsertion())
{
_consequences.Add(ConsequenceTag.inframe_insertion);
}
// InframeDeletion
if (_variantEffect.IsInframeDeletion())
{
_consequences.Add(ConsequenceTag.inframe_deletion);
}
// MissenseVariant
if (_variantEffect.IsMissenseVariant())
{
_consequences.Add(ConsequenceTag.missense_variant);
}
// ProteinAlteringVariant
if (_variantEffect.IsProteinAlteringVariant())
{
_consequences.Add(ConsequenceTag.protein_altering_variant);
}
// SpliceRegionVariant
if (_variantEffect.IsSpliceRegionVariant())
{
_consequences.Add(ConsequenceTag.splice_region_variant);
}
// IncompleteTerminalCodonVariant
if (_variantEffect.IsIncompleteTerminalCodonVariant())
{
_consequences.Add(ConsequenceTag.incomplete_terminal_codon_variant);
}
// StartRetainedVariant
if (_variantEffect.IsStartRetained())
{
_consequences.Add(ConsequenceTag.start_retained_variant);
}
// StopRetainedVariant
if (_variantEffect.IsStopRetained())
{
_consequences.Add(ConsequenceTag.stop_retained_variant);
}
// SynonymousVariant
if (_variantEffect.IsSynonymousVariant())
{
_consequences.Add(ConsequenceTag.synonymous_variant);
}
// CodingSequenceVariant
if (_variantEffect.IsCodingSequenceVariant())
{
_consequences.Add(ConsequenceTag.coding_sequence_variant);
}
// FivePrimeUtrVariant
if (_variantEffect.IsFivePrimeUtrVariant())
{
_consequences.Add(ConsequenceTag.five_prime_UTR_variant);
}
// ThreePrimeUtrVariant
if (_variantEffect.IsThreePrimeUtrVariant())
{
_consequences.Add(ConsequenceTag.three_prime_UTR_variant);
}
// NonCodingTranscriptExonVariant
if (_variantEffect.IsNonCodingTranscriptExonVariant())
{
_consequences.Add(ConsequenceTag.non_coding_transcript_exon_variant);
}
// IntronVariant
if (_variantEffect.IsWithinIntron())
{
_consequences.Add(ConsequenceTag.intron_variant);
}
// NonsenseMediatedDecayTranscriptVariant
if (_variantEffect.IsNonsenseMediatedDecayTranscriptVariant())
{
_consequences.Add(ConsequenceTag.NMD_transcript_variant);
}
// NonCodingTranscriptVariant
if (_variantEffect.IsNonCodingTranscriptVariant())
{
_consequences.Add(ConsequenceTag.non_coding_transcript_variant);
}
// FeatureElongation
if (_featureEffect.Elongation())
{
_consequences.Add(ConsequenceTag.feature_elongation);
}
// TranscriptTruncation
if (_featureEffect.Truncation())
{
_consequences.Add(ConsequenceTag.transcript_truncation);
}
}
