public void GetCdnaPositionOffset_Gap_Forward_ReturnNull()
{
var regions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Gap, 1, 134901, 135802, 1760, 2661)
};
var translation = new Mock <ITranslation>();
translation.SetupGet(x => x.CodingRegion).Returns(new CodingRegion(138530, 139309, 71, 850, 780));
var transcript = new Mock <ITranscript>();
transcript.SetupGet(x => x.Start).Returns(134901);
transcript.SetupGet(x => x.End).Returns(139379);
transcript.SetupGet(x => x.Gene.OnReverseStrand).Returns(false);
transcript.SetupGet(x => x.TranscriptRegions).Returns(regions);
transcript.SetupGet(x => x.Translation).Returns(translation.Object);
var po = HgvsUtilities.GetCdnaPositionOffset(transcript.Object, 135001, 0, false);
Assert.NotNull(po);
Assert.True(po.HasStopCodonNotation);
Assert.Equal(0, po.Offset);
Assert.Equal(1760, po.Position);
Assert.Equal("*910", po.Value);
}
public void GetCdnaPositionOffset_Intron_LeqR_Reverse()
{
var regions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 2, 134901, 135802, 1760, 2661),
new TranscriptRegion(TranscriptRegionType.Intron, 1, 135803, 137619, 1759, 1760),
new TranscriptRegion(TranscriptRegionType.Exon, 1, 137620, 139379, 1, 1759)
};
var translation = new Mock <ITranslation>();
translation.SetupGet(x => x.CodingRegion).Returns(new CodingRegion(138530, 139309, 71, 850, 780));
var transcript = new Mock <ITranscript>();
transcript.SetupGet(x => x.Start).Returns(134901);
transcript.SetupGet(x => x.End).Returns(139379);
transcript.SetupGet(x => x.Gene.OnReverseStrand).Returns(true);
transcript.SetupGet(x => x.TranscriptRegions).Returns(regions);
transcript.SetupGet(x => x.Translation).Returns(translation.Object);
var po = HgvsUtilities.GetCdnaPositionOffset(transcript.Object, 136711, 1, true);
Assert.NotNull(po);
Assert.True(po.HasStopCodonNotation);
Assert.Equal(909, po.Offset);
Assert.Equal(1759, po.Position);
Assert.Equal("*909+909", po.Value);
}
public void GetCdnaPositionOffset_Intron_ReqL_Reverse()
{
var regions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Intron, 10, 108901173, 108918171, 422, 423)
};
var translation = new Mock <ITranslation>();
translation.SetupGet(x => x.CodingRegion).Returns(new CodingRegion(108813927, 108941437, 129, 1613, 1485));
var transcript = new Mock <ITranscript>();
transcript.SetupGet(x => x.Start).Returns(108810721);
transcript.SetupGet(x => x.End).Returns(108918171);
transcript.SetupGet(x => x.Gene.OnReverseStrand).Returns(true);
transcript.SetupGet(x => x.TranscriptRegions).Returns(regions);
transcript.SetupGet(x => x.Translation).Returns(translation.Object);
var po = HgvsUtilities.GetCdnaPositionOffset(transcript.Object, 108909672, 0, true);
Assert.NotNull(po);
Assert.False(po.HasStopCodonNotation);
Assert.Equal(8500, po.Offset);
Assert.Equal(422, po.Position);
Assert.Equal("294+8500", po.Value);
}
public void GetCdnaPositionOffset_Exon_Reverse()
{
var transcript = HgvsCodingNomenclatureTests.GetReverseTranscript();
var po = HgvsUtilities.GetCdnaPositionOffset(transcript, 137721, 2, true);
Assert.NotNull(po);
Assert.True(po.HasStopCodonNotation);
Assert.Equal(0, po.Offset);
Assert.Equal(1659, po.Position);
Assert.Equal("*809", po.Value);
}
public void GetCdnaPositionOffset_Exon_Forward()
{
var transcript = HgvsCodingNomenclatureTests.GetForwardTranscript();
var po = HgvsUtilities.GetCdnaPositionOffset(transcript, 1262627, 4, true);
Assert.NotNull(po);
Assert.False(po.HasStopCodonNotation);
Assert.Equal(0, po.Offset);
Assert.Equal(540, po.Position);
Assert.Equal("129", po.Value);
}
public void GetCdnaPositionOffset_Intron_LeqR_Forward()
{
var transcript = HgvsCodingNomenclatureTests.GetForwardTranscript();
var po = HgvsUtilities.GetCdnaPositionOffset(transcript, 1261349, 1, true);
Assert.NotNull(po);
Assert.False(po.HasStopCodonNotation);
Assert.Equal(867, po.Offset);
Assert.Equal(336, po.Position);
Assert.Equal("-76+867", po.Value);
}
public void GetCdnaPositionOffset_Gap_RightSide_Reverse()
{
var transcript = GetReverseGapTranscript();
var po = HgvsUtilities.GetCdnaPositionOffset(transcript, 1103, 1, false);
Assert.NotNull(po);
Assert.False(po.HasStopCodonNotation);
Assert.Equal(0, po.Offset);
Assert.Equal(200, po.Position);
Assert.Equal("150", po.Value);
}
public void GetCdnaPositionOffset_Gap_RightSide_Forward()
{
var transcript = GetForwardGapTranscript();
var po = HgvsUtilities.GetCdnaPositionOffset(transcript, 1102, 1, true);
Assert.NotNull(po);
Assert.False(po.HasStopCodonNotation);
Assert.Equal(0, po.Offset);
Assert.Equal(101, po.Position);
Assert.Equal("51", po.Value);
}
public void GetCdnaPositionOffset_Intron_LltR_Reverse()
{
var transcript = HgvsCodingNomenclatureTests.GetReverseTranscript();
var po = HgvsUtilities.GetCdnaPositionOffset(transcript, 136000, 1, true);
Assert.NotNull(po);
Assert.True(po.HasStopCodonNotation);
Assert.Equal(-198, po.Offset);
Assert.Equal(1760, po.Position);
Assert.Equal("*910-198", po.Value);
}
public void GetCdnaPositionOffset_Intron_RltL_Reverse()
{
var transcript = HgvsCodingNomenclatureTests.GetReverseTranscript();
var po = HgvsUtilities.GetCdnaPositionOffset(transcript, 137619, 1, true);
Assert.NotNull(po);
Assert.True(po.HasStopCodonNotation);
Assert.Equal(2, po.Offset);
Assert.Equal(1759, po.Position);
Assert.Equal("*909+2", po.Value);
}
public void GetCdnaPositionOffset_Intron_RltL_Forward()
{
var transcript = HgvsCodingNomenclatureTests.GetForwardTranscript();
var po = HgvsUtilities.GetCdnaPositionOffset(transcript, 1262210, 1);
Assert.NotNull(po);
Assert.False(po.HasStopCodonNotation);
Assert.Equal(-6, po.Offset);
Assert.Equal(337, po.Position);
Assert.Equal("-75-6", po.Value);
}
private static (string Hgvs, bool IsTranscriptSuffix) GetBreakEndHgvs(ITranscript transcript, int regionIndex,
int position, bool isGenomicSuffix)
{
var positionOffset = HgvsUtilities.GetCdnaPositionOffset(transcript, position, regionIndex);
var isTranscriptSuffix = isGenomicSuffix != transcript.Gene.OnReverseStrand;
var codingRegionLength = transcript.Translation.CodingRegion.CdnaEnd - transcript.Translation.CodingRegion.CdnaStart + 1;
var hgvsPosString = isTranscriptSuffix ? positionOffset.Value + "_" + codingRegionLength : 1 + "_" + positionOffset.Value;
var hgvs = transcript.Gene.Symbol + "{" + transcript.Id.WithVersion + "}" + ":c." + hgvsPosString;
return(hgvs, isTranscriptSuffix);
}
private static (string Begin, string End) AdjustSecond(BreakPointTranscript second)
{
var codingRegion = second.Transcript.Translation.CodingRegion;
int position = second.GenomicPosition;
int codingRegionLength = codingRegion.CdnaEnd - codingRegion.CdnaStart + 1;
if (position < codingRegion.Start)
{
return((position - codingRegion.Start).ToString(), "?");
}
if (position > codingRegion.End)
{
return((position - codingRegion.End + codingRegionLength).ToString(), "?");
}
return(HgvsUtilities.GetCdnaPositionOffset(second.Transcript, position, second.RegionIndex).Value, codingRegionLength.ToString());
}
private static (string Begin, string End) AdjustFirst(BreakPointTranscript first)
{
var codingRegion = first.Transcript.Translation.CodingRegion;
int position = first.GenomicPosition;
int codingRegionLength = codingRegion.CdnaEnd - codingRegion.CdnaStart + 1;
if (position < codingRegion.Start)
{
return("?", (position - codingRegion.Start).ToString());
}
if (position > codingRegion.End)
{
return("?", (position - codingRegion.End + codingRegionLength).ToString());
}
return("1", HgvsUtilities.GetCdnaPositionOffset(first.Transcript, position, first.RegionIndex).Value);
}
