public void FindRegion_Forward_Insertion()
{
var observedStart = MappedPositionUtilities.FindRegion(_forwardTranscriptRegions, ForwardVariantStart);
var observedEnd = MappedPositionUtilities.FindRegion(_forwardTranscriptRegions, ForwardVariantEnd);
Assert.Equal(4, observedStart.Index);
Assert.Equal(4, observedEnd.Index);
Assert.NotNull(observedStart.Region);
Assert.NotNull(observedEnd.Region);
}
public void FindRegion_Reverse_Deletion()
{
var observedStart = MappedPositionUtilities.FindRegion(_reverseTranscriptRegions, ReverseVariantStart);
var observedEnd = MappedPositionUtilities.FindRegion(_reverseTranscriptRegions, ReverseVariantEnd);
Assert.Equal(6, observedStart.Index);
Assert.Equal(7, observedEnd.Index);
Assert.NotNull(observedStart.Region);
Assert.NotNull(observedEnd.Region);
}
private static IMappedPosition GetMappedPosition(ITranscriptRegion[] regions, IInterval variant)
{
(int startIndex, _) = MappedPositionUtilities.FindRegion(regions, variant.Start);
(int endIndex, _) = MappedPositionUtilities.FindRegion(regions, variant.End);
(int exonStart, int exonEnd, int intronStart, int intronEnd) = regions.GetExonsAndIntrons(startIndex, endIndex);
return(new MappedPosition(-1, -1, -1, -1, -1, -1, exonStart, exonEnd, intronStart, intronEnd, startIndex,
endIndex));
}
/// <summary>
/// Adjust positions by alt allele length
/// </summary>
internal static (int Start, int End, string RefAllele, int RegionStart, int RegionEnd) ShiftDuplication(
this ITranscriptRegion[] regions, int start, string altAllele, bool onReverseStrand)
{
int incrementLength = altAllele.Length;
int dupStart = onReverseStrand ? start + incrementLength - 1 : start - incrementLength;
int dupEnd = onReverseStrand ? dupStart - incrementLength + 1 : dupStart + incrementLength - 1;
(int regionStart, _) = MappedPositionUtilities.FindRegion(regions, dupStart);
(int regionEnd, _) = MappedPositionUtilities.FindRegion(regions, dupEnd);
return(dupStart, dupEnd, altAllele, regionStart, regionEnd);
}
public void GetHgvscAnnotation_in_intron_gap_substitution(int variantStart, int variantEnd, string reference, string alt,
string transcriptRef, VariantType variantType, string expectedHgvsc)
{
var(startIndex, _) =
MappedPositionUtilities.FindRegion(_gapTranscript.TranscriptRegions, variantStart);
var(endIndex, _) =
MappedPositionUtilities.FindRegion(_gapTranscript.TranscriptRegions, variantEnd);
var variant = new SimpleVariant(ChromosomeUtilities.Chr10, variantStart, variantEnd, reference, alt, variantType);
var observedHgvsc =
HgvsCodingNomenclature.GetHgvscAnnotation(_gapTranscript, variant, null, startIndex, endIndex, transcriptRef, null);
Assert.Equal(expectedHgvsc, observedHgvsc);
}
internal static void GetGeneFusionsByTranscript(this Dictionary <string, IAnnotatedGeneFusion> transcriptIdToGeneFusions,
BreakEndAdjacency adjacency, ITranscript[] originTranscripts, ITranscript[] partnerTranscripts)
{
var geneFusions = new List <IGeneFusion>();
foreach (var originTranscript in originTranscripts)
{
geneFusions.Clear();
bool originOnReverseStrand = originTranscript.Gene.OnReverseStrand ^ adjacency.Origin.OnReverseStrand;
(int originIndex, ITranscriptRegion originRegion) = MappedPositionUtilities.FindRegion(originTranscript.TranscriptRegions, adjacency.Origin.Position);
int?originExon = originRegion.Type == TranscriptRegionType.Exon ? (int?)originRegion.Id : null;
int?originIntron = originRegion.Type == TranscriptRegionType.Intron ? (int?)originRegion.Id : null;
foreach (var partnerTranscript in partnerTranscripts)
{
bool partnerOnReverseStrand = partnerTranscript.Gene.OnReverseStrand ^ adjacency.Partner.OnReverseStrand;
bool differentStrand = originOnReverseStrand != partnerOnReverseStrand;
bool differentTranscriptSource = originTranscript.Source != partnerTranscript.Source;
bool sameGeneSymbol = originTranscript.Gene.Symbol == partnerTranscript.Gene.Symbol;
bool codingRegionAlreadyOverlaps = originTranscript.Translation.CodingRegion.Overlaps(partnerTranscript.Translation.CodingRegion);
if (differentStrand || differentTranscriptSource || sameGeneSymbol || codingRegionAlreadyOverlaps)
{
continue;
}
(int partnerIndex, ITranscriptRegion partnerRegion) = MappedPositionUtilities.FindRegion(partnerTranscript.TranscriptRegions, adjacency.Partner.Position);
int?partnerExon = partnerRegion.Type == TranscriptRegionType.Exon ? (int?)partnerRegion.Id : null;
int?partnerIntron = partnerRegion.Type == TranscriptRegionType.Intron ? (int?)partnerRegion.Id : null;
BreakPointTranscript origin = new BreakPointTranscript(originTranscript, adjacency.Origin.Position, originIndex);
BreakPointTranscript partner = new BreakPointTranscript(partnerTranscript, adjacency.Partner.Position, partnerIndex);
(BreakPointTranscript first, BreakPointTranscript second) = originOnReverseStrand ? (partner, origin) : (origin, partner);
string hgvsCoding = GetHgvsCoding(first, second);
geneFusions.Add(new GeneFusion(partnerExon, partnerIntron, hgvsCoding));
}
if (geneFusions.Count == 0)
{
continue;
}
var annotatedGeneFusion = new AnnotatedGeneFusion(originExon, originIntron, geneFusions.ToArray());
transcriptIdToGeneFusions[originTranscript.Id.WithVersion] = annotatedGeneFusion;
}
}
AltAminoAcids, string RefCodons, string AltCodons, string TranscriptAltAllele, string TranscriptRefAllele) AnnotateTranscript(ITranscript transcript, ISimpleVariant variant, AminoAcids aminoAcids, ISequence refSequence)
{
bool onReverseStrand = transcript.Gene.OnReverseStrand;
var start = MappedPositionUtilities.FindRegion(transcript.TranscriptRegions, variant.Start);
var end = MappedPositionUtilities.FindRegion(transcript.TranscriptRegions, variant.End);
var position = GetMappedPosition(transcript.TranscriptRegions, start.Region, start.Index, end.Region,
end.Index, variant, onReverseStrand, transcript.Translation?.CodingRegion, transcript.StartExonPhase,
variant.Type == VariantType.insertion);
var codingSequence = GetCodingSequence(transcript, refSequence);
var cdnaSequence = GetCdnaSequence(transcript, refSequence);
string transcriptAltAllele = HgvsUtilities.GetTranscriptAllele(variant.AltAllele, onReverseStrand);
var codons = Codons.GetCodons(transcriptAltAllele, position.CdsStart, position.CdsEnd, position.ProteinStart, position.ProteinEnd, codingSequence);
var aa = aminoAcids.Translate(codons.Reference, codons.Alternate);
(aa, position.ProteinStart, position.ProteinEnd) = TryTrimAminoAcidsAndUpdateProteinPositions(aa, position.ProteinStart, position.ProteinEnd);
(position.CoveredCdnaStart, position.CoveredCdnaEnd) = transcript.TranscriptRegions.GetCoveredCdnaPositions(position.CdnaStart, start.Index, position.CdnaEnd, end.Index, onReverseStrand);
(position.CoveredCdsStart, position.CoveredCdsEnd, position.CoveredProteinStart, position.CoveredProteinEnd) = MappedPositionUtilities.GetCoveredCdsAndProteinPositions(position.CoveredCdnaStart, position.CoveredCdnaEnd, transcript.StartExonPhase, transcript.Translation?.CodingRegion);
var transcriptRefAllele = GetTranscriptRefAllele(position, cdnaSequence, variant, onReverseStrand);
SequenceChange coveredAa;
// only generate the covered version of ref & alt alleles when CDS start/end is -1
if (position.CdsStart == -1 || position.CdsEnd == -1)
{
coveredAa = GetCoveredAa(aminoAcids, transcriptAltAllele, position.CoveredCdsStart, position.CoveredCdsEnd, position.CoveredProteinStart, position.CoveredProteinEnd, codingSequence);
(coveredAa, position.CoveredProteinStart, position.CoveredProteinEnd) = TryTrimAminoAcidsAndUpdateProteinPositions(coveredAa, position.CoveredProteinStart, position.CoveredProteinEnd);
}
else
{
coveredAa = aa;
position.CoveredProteinStart = position.ProteinStart;
position.CoveredProteinEnd = position.ProteinEnd;
}
var positionalEffect = GetPositionalEffect(transcript, variant, position, aa.Reference, aa.Alternate,
position.CoveredCdnaStart, position.CoveredCdnaEnd, position.CoveredCdsStart, position.CoveredCdsEnd);
var variantEffect = new VariantEffect(positionalEffect, variant, transcript, aa.Reference, aa.Alternate,
codons.Reference, codons.Alternate, position.ProteinStart, coveredAa.Reference, coveredAa.Alternate);
return(variantEffect, position, aa.Reference, aa.Alternate, codons.Reference, codons.Alternate, transcriptAltAllele, transcriptRefAllele);
}
AltAminoAcids, string RefCodons, string AltCodons, string TranscriptAltAllele) AnnotateTranscript(ITranscript transcript, ISimpleVariant variant, AminoAcids aminoAcids,
ISequence refSequence)
{
var onReverseStrand = transcript.Gene.OnReverseStrand;
var start = MappedPositionUtilities.FindRegion(transcript.TranscriptRegions, variant.Start);
var end = MappedPositionUtilities.FindRegion(transcript.TranscriptRegions, variant.End);
var position = GetMappedPosition(transcript.TranscriptRegions, start.Region, start.Index, end.Region,
end.Index, variant, onReverseStrand, transcript.Translation?.CodingRegion, transcript.StartExonPhase,
variant.Type == VariantType.insertion);
var transcriptRefAllele = HgvsUtilities.GetTranscriptAllele(variant.RefAllele, onReverseStrand);
var transcriptAltAllele = HgvsUtilities.GetTranscriptAllele(variant.AltAllele, onReverseStrand);
var codingSequence = transcript.Translation == null
? null
: new CodingSequence(refSequence, transcript.Translation.CodingRegion, transcript.TranscriptRegions,
transcript.Gene.OnReverseStrand, transcript.StartExonPhase);
var codons = Codons.GetCodons(transcriptRefAllele, transcriptAltAllele, position.CdsStart, position.CdsEnd,
position.ProteinStart, position.ProteinEnd, codingSequence);
var coveredCdna = transcript.TranscriptRegions.GetCoveredCdnaPositions(position.CdnaStart, start.Index,
position.CdnaEnd, end.Index, onReverseStrand);
var coveredCds = MappedPositionUtilities.GetCoveredCdsPositions(coveredCdna.Start, coveredCdna.End,
transcript.StartExonPhase, transcript.Translation?.CodingRegion);
var aa = aminoAcids.Translate(codons.Reference, codons.Alternate);
var positionalEffect = GetPositionalEffect(transcript, variant, position, aa.Reference, aa.Alternate,
coveredCdna.Start, coveredCdna.End, coveredCds.Start, coveredCds.End);
var variantEffect = new VariantEffect(positionalEffect, variant, transcript, aa.Reference, aa.Alternate,
codons.Reference, codons.Alternate, position.ProteinStart);
return(variantEffect, position, aa.Reference, aa.Alternate, codons.Reference, codons.Alternate,
transcriptAltAllele);
}
internal static IGeneFusionAnnotation GetGeneFusionAnnotation(IBreakEnd[] breakEnds, ITranscript transcript,
ITranscript[] fusedTranscriptCandidates)
{
if (transcript.Translation == null || breakEnds == null || breakEnds.Length == 0)
{
return(null);
}
var desiredBreakEnd = GetBreakEndWithinCodingRegion(breakEnds, transcript.Chromosome, transcript.Translation.CodingRegion);
if (desiredBreakEnd == null)
{
return(null);
}
var piece1 = MappedPositionUtilities.FindRegion(transcript.TranscriptRegions, desiredBreakEnd.Piece1.Position);
int?exon = piece1.Region.Type == TranscriptRegionType.Exon ? (int?)piece1.Region.Id : null;
int?intron = piece1.Region.Type == TranscriptRegionType.Intron ? (int?)piece1.Region.Id : null;
var piece1Hgvs = GetBreakEndHgvs(transcript, piece1.Index, desiredBreakEnd.Piece1.Position, desiredBreakEnd.Piece1.IsSuffix);
var geneFusions = new List <IGeneFusion>();
foreach (var candidate in fusedTranscriptCandidates)
{
var piece2 = MappedPositionUtilities.FindRegion(candidate.TranscriptRegions, desiredBreakEnd.Piece2.Position);
var geneFusion = GetGeneFusion(transcript, candidate, desiredBreakEnd.Piece2, piece2.Index,
piece1Hgvs.Hgvs, piece1Hgvs.IsTranscriptSuffix);
if (geneFusion != null)
{
geneFusions.Add(geneFusion);
}
}
return(geneFusions.Count == 0
? null
: new GeneFusionAnnotation(exon, intron, geneFusions.ToArray()));
}