/// <summary>
/// Did we gain a start codon in this 5'UTR interval?
/// </summary>
/// <param name="seqChange"></param>
/// <returns>A new start codon (if gained)</returns>
private string startGained(Variant seqChange)
{
if (!seqChange.isSnv())
{
return("");
} // Only SNPs supported.
// Calculate SNP position relative to UTRs
long pos = seqChange.DistanceBases(get5primeUtrs().OfType <Interval>().ToList(), IsStrandMinus());
// Change base at SNP position
string sequence = getSequence();
char[] chars = sequence.ToCharArray();
char snpBase = seqChange.NetChange(this)[0];
if (IsStrandMinus() && Alphabets.DNA.TryGetComplementSymbol((byte)snpBase, out byte complement))
{
snpBase = (char)complement;
}
chars[pos] = snpBase;
// Do we gain a new start codon?
return(startGained(chars, pos));
}
/// <summary>
/// Return functional class of this effect (i.e. NONSENSE, MISSENSE, SILENT or NONE)
/// </summary>
/// <returns></returns>
public FunctionalClass GetFunctionalClass()
{
if (Variant.isSnv())
{
if (!AlternateAA.Equals(ReferenceAA))
{
Translation.TranslateDnaCodon(CodonsAlt, out byte aa);
return(aa == Alphabets.Protein.Ter ?
FunctionalClass.NONSENSE :
FunctionalClass.MISSENSE);
}
if (!CodonsAlt.Equals(CodonsRef))
{
return(FunctionalClass.SILENT);
}
}
return(FunctionalClass.NONE);
}
/// <summary>
/// Calculate additional effect due to codon changes, e.g. A frame-shift that also affects a stop codon
/// </summary>
/// <param name="codonsOld"></param>
/// <param name="codonsNew"></param>
/// <param name="codonNum"></param>
/// <param name="codonIndex"></param>
/// <returns></returns>
protected EffectType AdditionalEffect(string codonsOld, string codonsNew, int codonNum, int codonIndex)
{
EffectType newEffectType = EffectType.NONE;
bool hasOldAa = CodonExtensions.TryTranslateCodon(Transcript.Gene.Chromosome.Mitochondrial, codonsOld, out byte oldAA);
bool hasNewAa = CodonExtensions.TryTranslateCodon(Transcript.Gene.Chromosome.Mitochondrial, codonsNew, out byte newAA);
bool isStartNew = Transcript.Gene.Chromosome.Mitochondrial ?
CodonsVertebrateMitochondrial.START_CODONS.Contains(codonsNew.ToUpper(CultureInfo.InvariantCulture)) :
CodonsStandard.START_CODONS.Contains(codonsNew.ToUpper(CultureInfo.InvariantCulture));
bool isStartOld = Transcript.Gene.Chromosome.Mitochondrial ?
CodonsVertebrateMitochondrial.START_CODONS.Contains(codonsOld.ToUpper(CultureInfo.InvariantCulture)) :
CodonsStandard.START_CODONS.Contains(codonsOld.ToUpper(CultureInfo.InvariantCulture));
bool isStopOld = hasOldAa && oldAA == Alphabets.Protein.Ter;
bool isStopNew = hasNewAa && newAA == Alphabets.Protein.Ter;
if (Variant.isSnv() || Variant.isMnv())
{
// SNM and MNP effects
if (oldAA.Equals(newAA))
{
// Same AA: Synonymous coding
if (codonNum == 0 && isStartOld)
{
// It is in the first codon (which also is a start codon)
if (isStartNew)
{
newEffectType = EffectType.SYNONYMOUS_START;
} // The new codon is also a start codon => SYNONYMOUS_START
else
{
newEffectType = EffectType.START_LOST;
} // The AA is the same, but the codon is not a start codon => start lost
}
else if (isStopOld)
{
// Stop codon
if (isStopNew)
{
newEffectType = EffectType.SYNONYMOUS_STOP;
} // New codon is also a stop => SYNONYMOUS_STOP
else
{
newEffectType = EffectType.STOP_LOST;
} // New codon is not a stop, the we've lost a stop
}
else
{
newEffectType = EffectType.SYNONYMOUS_CODING; // All other cases are just SYNONYMOUS_CODING
}
}
else
{
// Different AA: Non-synonymous coding
if ((codonNum == 0) && isStartOld)
{
// It is in the first codon (which also is a start codon)
if (isStartNew)
{
newEffectType = EffectType.NON_SYNONYMOUS_START;
} // Non-synonymous mutation on first codon => start lost
else
{
newEffectType = EffectType.START_LOST;
} // Non-synonymous mutation on first codon => start lost
}
else if (isStopOld)
{
// Stop codon
if (isStopNew)
{
newEffectType = EffectType.NON_SYNONYMOUS_STOP;
} // Notice: This should never happen for SNPs! (for some reason I removed this comment at some point and that create some confusion): http://www.biostars.org/post/show/51352/in-snpeff-impact-what-is-difference-between-stop_gained-and-non-synonymous_stop/
else
{
newEffectType = EffectType.STOP_LOST;
}
}
else if (isStopNew)
{
newEffectType = EffectType.STOP_GAINED;
}
else
{
newEffectType = EffectType.NON_SYNONYMOUS_CODING; // All other cases are just NON_SYN
}
}
}
else
{
// Add a new effect in some cases
if ((codonNum == 0) && isStartOld && !isStartNew)
{
newEffectType = EffectType.START_LOST;
}
else if (isStopOld && !isStopNew)
{
newEffectType = EffectType.STOP_LOST;
}
else if (!isStopOld && isStopNew)
{
newEffectType = EffectType.STOP_GAINED;
}
}
return(newEffectType);
}