/// <summary>
/// returns the translated coding sequence including the variant and the 3' UTR
/// </summary>
private string GetTranslatedCodingSequence(TranscriptAnnotation ta)
{
// get the sequence with the variant added
string altCds = TranscriptUtilities.GetAlternateCds(_compressedSequence, ta.CodingDnaSequenceBegin,
ta.CodingDnaSequenceEnd, ta.TranscriptAlternateAllele, _transcript.CdnaMaps,
_transcript.Gene.OnReverseStrand, _transcript.StartExonPhase,
_transcript.Translation.CodingRegion.CdnaStart);
if (string.IsNullOrEmpty(altCds))
{
return(null);
}
// get the new translation
return(_aminoAcids.TranslateBases(altCds, true));
}
/// <summary>
/// get the shorted intron offset from the nearest exon
/// </summary>
private void GetIntronOffset(CdnaCoordinateMap prevExon, CdnaCoordinateMap exon, int?position, PositionOffset po)
{
int?upDist = position - prevExon.GenomicEnd;
int?downDist = exon.GenomicStart - position;
int tempCdnaBegin, tempCdnaEnd;
if (upDist < downDist || upDist == downDist && !_transcript.Gene.OnReverseStrand)
{
// distance to upstream exon is the shortest (or equal and in the positive orientation)
TranscriptUtilities.GetCodingDnaEndpoints(_transcript.CdnaMaps, prevExon.GenomicStart,
prevExon.GenomicEnd, out tempCdnaBegin, out tempCdnaEnd);
if (_transcript.Gene.OnReverseStrand)
{
po.Position = tempCdnaBegin;
po.Offset = -upDist;
}
else
{
po.Position = tempCdnaEnd;
po.Offset = upDist;
}
}
else
{
// distance to downstream exon is the shortest
TranscriptUtilities.GetCodingDnaEndpoints(_transcript.CdnaMaps, exon.GenomicStart, exon.GenomicEnd,
out tempCdnaBegin, out tempCdnaEnd);
if (_transcript.Gene.OnReverseStrand)
{
po.Position = tempCdnaEnd;
po.Offset = downDist;
}
else
{
po.Position = tempCdnaBegin;
po.Offset = -downDist;
}
}
}
/// <summary>
/// gets the variant position (with intron offset) in the transcript [TranscriptVariationAllele.pm:1805 _get_cDNA_position]
/// </summary>
private void GetCdnaPosition(PositionOffset po)
{
int?position = po.Position;
// start and stop coordinate relative to transcript. Take into account which
// strand we're working on
position = _transcript.Gene.OnReverseStrand
? _transcript.End - position + 1
: _transcript.Start + position - 1;
// loop over the exons and get the coordinates of the variation in exon+intron notation
var exons = _transcript.CdnaMaps;
for (int exonIndex = 0; exonIndex < exons.Length; exonIndex++)
{
var exon = exons[exonIndex];
// skip if the start point is beyond this exon
if (position > exon.GenomicEnd)
{
continue;
}
// EXONIC: if the start coordinate is within this exon
if (position >= exon.GenomicStart)
{
// get the cDNA start coordinate of the exon and add the number of nucleotides
// from the exon boundary to the variation. If the transcript is in the opposite
// direction, count from the end instead
int tempCdnaEnd, tempCdnaBegin;
TranscriptUtilities.GetCodingDnaEndpoints(_transcript.CdnaMaps, exon.GenomicStart, exon.GenomicEnd,
out tempCdnaBegin, out tempCdnaEnd);
po.Position = tempCdnaBegin + (_transcript.Gene.OnReverseStrand
? exon.GenomicEnd - position
: position - exon.GenomicStart);
break;
}
// INTRONIC: the start coordinate is between this exon and the previous one, determine which one is closest and get coordinates relative to that one
// sanity check: make sure we have at least passed one exon
if (exonIndex < 1)
{
po.Position = null;
return;
}
var prevExon = exons[exonIndex - 1];
GetIntronOffset(prevExon, exon, position, po);
break;
}
// start by correcting for the stop codon
int startCodon = _transcript.Translation == null ? -1 : _transcript.Translation.CodingRegion.CdnaStart;
int stopCodon = _transcript.Translation == null ? -1 : _transcript.Translation.CodingRegion.CdnaEnd;
string cdnaCoord = po.Position.ToString();
po.HasStopCodonNotation = false;
bool hasNoPosition = false;
if (stopCodon != -1)
{
if (po.Position > stopCodon)
{
cdnaCoord = '*' + (po.Position - stopCodon).ToString();
po.HasStopCodonNotation = true;
}
else if (po.Offset != null && po.Position == stopCodon)
{
cdnaCoord = "*";
po.HasStopCodonNotation = true;
hasNoPosition = true;
}
}
if (!po.HasStopCodonNotation && startCodon != -1)
{
cdnaCoord = (po.Position + (po.Position >= startCodon ? 1 : 0) - startCodon).ToString();
}
// re-assemble the cDNA position [ return exon num & offset & direction for intron eg. 142+363]
if (hasNoPosition)
{
po.Value = "*" + po.Offset;
}
else
{
po.Value = cdnaCoord + (po.Offset == null ? "" : ((int)po.Offset).ToString("+0;-0;+0"));
}
}
