/// <summary>
/// assigns the reference and alternate codons [TranscriptVariationAllele.pm:259 codon]
/// </summary>
public static void Assign(TranscriptAnnotation ta, Transcript transcript, ICompressedSequence compressedSequence)
{
// sanity check: make sure this is a coding region
if (!(ta.HasValidCdsEnd && ta.HasValidCdsStart))
{
ta.ReferenceCodon = null;
ta.AlternateCodon = null;
return;
}
// calculate necessary coordinates and lengths
int aminoAcidStart = ta.ProteinBegin * 3 - 2;
int aminoAcidEnd = ta.ProteinEnd * 3;
int prefixLen = ta.CodingDnaSequenceBegin - aminoAcidStart;
int suffixLen = aminoAcidEnd - ta.CodingDnaSequenceEnd;
var codingSequence = new CodingSequence(compressedSequence, transcript.Translation.CodingRegion.GenomicStart,
transcript.Translation.CodingRegion.GenomicEnd, transcript.CdnaMaps, transcript.Gene.OnReverseStrand,
transcript.StartExonPhase);
var aminoAcidSeq = codingSequence.Sequence();
int start1 = aminoAcidStart - 1;
int start2 = aminoAcidEnd - suffixLen;
int maxSuffixLen = aminoAcidSeq.Length - start2;
bool atTailEnd = false;
if (suffixLen > maxSuffixLen)
{
suffixLen = maxSuffixLen;
atTailEnd = true;
}
if (start1 < 0)
{
start1 = 0;
}
if (start2 < 0)
{
start2 = 0;
}
if (prefixLen < 0)
{
prefixLen = 0;
}
string prefix = start1 + prefixLen < aminoAcidSeq.Length
? aminoAcidSeq.Substring(start1, prefixLen).ToLower()
: "AAA";
string suffix = suffixLen > 0
? aminoAcidSeq.Substring(start2, suffixLen).ToLower()
: "";
ta.HasFrameShift = false;
ta.ReferenceCodon = GetCodon(ta.TranscriptReferenceAllele, prefix, suffix, ref ta.HasFrameShift, atTailEnd);
ta.AlternateCodon = GetCodon(ta.TranscriptAlternateAllele, prefix, suffix, ref ta.HasFrameShift, atTailEnd);
}
/// <summary>O
/// sets the amino acids given the reference and variant codons
/// </summary>
public void Assign(TranscriptAnnotation transcriptAnnotation)
{
if (string.IsNullOrEmpty(transcriptAnnotation.ReferenceCodon) &&
string.IsNullOrEmpty(transcriptAnnotation.AlternateCodon))
{
return;
}
// sanity check: return null if either codon contains Ns
if (transcriptAnnotation.ReferenceCodon.Contains("N") ||
transcriptAnnotation.AlternateCodon.Contains("N"))
{
return;
}
transcriptAnnotation.ReferenceAminoAcids = TranslateBases(transcriptAnnotation.ReferenceCodon, false);
transcriptAnnotation.AlternateAminoAcids = TranslateBases(transcriptAnnotation.AlternateCodon, false);
}
