/// <summary>
/// Create a specific codon change for a variant
/// </summary>
/// <param name="variant"></param>
/// <param name="transcript"></param>
/// <param name="variantEffects"></param>
/// <returns></returns>
public static CodonChange Factory(Variant variant, Transcript transcript, VariantEffects variantEffects)
{
switch (variant.VarType)
{
case Variant.VariantType.SNV:
return(new CodonChangeSnv(variant, transcript, variantEffects));
case Variant.VariantType.INS:
return(new CodonChangeIns(variant, transcript, variantEffects));
case Variant.VariantType.DEL:
return(new CodonChangeDel(variant, transcript, variantEffects));
case Variant.VariantType.MNV:
return(new CodonChangeMnv(variant, transcript, variantEffects));
//case Variant.VariantType.MIXED:
// return new CodonChangeMixed(variant, transcript, variantEffects);
case Variant.VariantType.DUP:
return(new CodonChangeDup(variant, transcript, variantEffects));
case Variant.VariantType.INV:
return(new CodonChangeInv(variant, transcript, variantEffects));
case Variant.VariantType.INTERVAL:
return(new CodonChangeInterval(variant, transcript, variantEffects));
default:
throw new ArgumentException("Unimplemented factory for variant type '" + variant.VarType + "', variant: " + variant);
}
}
/// <summary>
/// Add an effect
/// </summary>
/// <param name="marker"></param>
/// <param name="effectType"></param>
/// <param name="effectImpact"></param>
/// <param name="codonsOld"></param>
/// <param name="codonsNew"></param>
/// <param name="codonNum"></param>
/// <param name="codonIndex"></param>
/// <param name="allowReplace"></param>
/// <returns></returns>
private VariantEffect Effect(Interval marker, EffectType effectType, EffectImpact effectImpact, string codonsOld, string codonsNew, int codonNum, int codonIndex, bool allowReplace)
{
// Create and add variant affect
long cDnaPos = Transcript.BaseNumber2MRnaPos(Variant.OneBasedStart);
VariantEffect varEff = new VariantEffect(Variant, marker, effectType, effectImpact, codonsOld, codonsNew, codonNum, codonIndex, cDnaPos);
VariantEffects.AddEffect(varEff);
// Are there any additional effects? Sometimes a new effect arises from setting codons (e.g. FRAME_SHIFT disrupts a STOP codon)
EffectType addEffType = AdditionalEffect(codonsOld, codonsNew, codonNum, codonIndex);
if (addEffType != EffectType.NONE && addEffType != effectType)
{
if (allowReplace && addEffType.CompareTo(effectType) < 0)
{
// Replace main effect (using default impact)
varEff.SetEffect(addEffType);
}
else
{
// Add effect to list (using default impact)
varEff.AddEffect(addEffType);
}
}
return(varEff);
}
public override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
if (!Intersects(variant))
{
return(false);
}
Transcript tr = (Transcript)Parent;
bool coding = tr.IsProteinCoding();
// Different analysis for coding or non-coding
bool exonAnnotated = false;
if (!coding || variant.isInterval() || !variant.isVariant())
{
// Non-coding or non-variant? Just annotate as 'exon'
variantEffects.AddEffect(variant, this, EffectType.EXON, "");
exonAnnotated = true;
}
else if (tr.IsCds(variant))
{
// Is it a coding transcript and the variant is within the CDS?
// => We need codon analysis
CodonChange codonChange = CodonChange.Factory(variant, tr, variantEffects);
codonChange.ChangeCodon();
exonAnnotated = true;
}
// Any splice site effect to add?
//for (SpliceSite ss : spliceSites)
// if (ss.intersects(variant)) ss.variantEffect(variant, variantEffects);
return(exonAnnotated);
}
public override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
// Has the whole UTR been deleted?
if (variant.Includes(this) && variant.VarType == Variant.VariantType.DEL)
{
variantEffects.AddEffect(variant, this, EffectType.UTR_5_DELETED, ""); // A UTR was removed entirely
return(true);
}
// Add distance
Transcript tr = (Transcript)FindParent(typeof(Transcript));
long distance = utrDistance(variant, tr);
VariantEffect variantEffect = new VariantEffect(variant);
variantEffect.Set(this, IntervalType, EffectTypeMethods.EffectDictionary[IntervalType], distance >= 0 ? distance + " bases from TSS" : "");
variantEffect.Distance = distance;
variantEffects.AddEffect(variantEffect);
// Start gained?
string gained = startGained(variant);
if (gained != "")
{
variantEffects.AddEffect(variant, this, EffectType.START_GAINED, gained);
}
return(true);
}
/// <summary>
/// Calculate the effect of this variant
/// </summary>
/// <param name="variant"></param>
/// <param name="variantEffects"></param>
/// <returns></returns>
public virtual bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
if (!Intersects(variant))
{
return(false);
}
variantEffects.AddEffect(variant, this, IntervalType, "");
return(true);
}
public override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
if (!Intersects(variant))
{
return(false);
}
//for (SpliceSite ss : spliceSites)
// if (ss.intersects(variant)) ss.variantEffect(variant, variantEffects);
// Add intron part
variantEffects.AddEffectType(variant, this, EffectType.INTRON);
return(true);
}
/// <summary>
/// Analyze SNPs in this transcript. Add changeEffect to 'changeEffect'
/// </summary>
/// <param name="exon"></param>
/// <returns></returns>
protected override bool ChangeCodon(Exon exon)
{
// Get old and new codons
CodonsReference = CodonsRef();
CodonsAlternate = CodonsAlt();
// Use a generic low priority variant, this allows 'AdditionalEffects' to override it
Effect(exon, EffectType.CODON_CHANGE, true);
if (CodonsReference == "")
{
VariantEffects.AddErrorWarning(Variant, ErrorWarningType.ERROR_MISSING_CDS_SEQUENCE);
}
return(true);
}
public override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
if (!Intersects(variant))
{
return(false);
}
if (variant.Includes(this) && variant.VarType == Variant.VariantType.DEL)
{
variantEffects.AddEffectType(variant, this, EffectType.UTR_3_DELETED); // A UTR was removed entirely
return(true);
}
Transcript tr = (Transcript)FindParent(typeof(Transcript));
long distance = utrDistance(variant, tr);
VariantEffect variantEffect = new VariantEffect(variant);
variantEffect.Set(this, EffectType.UTR_3_PRIME, EffectTypeMethods.EffectDictionary[EffectType.UTR_3_PRIME], distance >= 0 ? distance + " bases from CDS" : "");
variantEffect.Distance = distance;
variantEffects.AddEffect(variantEffect);
return(true);
}
public CodonChangeSnv(Variant variant, Transcript transcript, VariantEffects variantEffects)
: base(variant, transcript, variantEffects)
{
ReturnNow = true; // A SNP can only affect one exon
}
protected CodonChangeStructural(Variant variant, Transcript transcript, VariantEffects variantEffects)
: base(variant, transcript, variantEffects)
{
coding = transcript.IsProteinCoding(); // || Config.get().isTreatAllAsProteinCoding();
CountAffectedExons();
}
public abstract override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects);
public CodonChangeMnv(Variant variant, Transcript transcript, VariantEffects variantEffects)
: base(variant, transcript, variantEffects)
{
ReturnNow = false;
RequireNetCdsChange = true;
}
public CodonChangeIns(Variant seqChange, Transcript transcript, VariantEffects changeEffects)
: base(seqChange, transcript, changeEffects)
{
ReturnNow = true; // An insertion can only affect one exon
}
protected CodonChange(Variant variant, Transcript transcript, VariantEffects variantEffects)
{
Transcript = transcript;
VariantEffects = variantEffects;
Variant = variant;
}
/// <summary>
/// Calculate a list of codon changes
/// </summary>
public virtual void ChangeCodon()
{
if (!Transcript.Intersects(Variant))
{
return;
}
// Get coding start (after 5 prime UTR)
long cdsStart = Transcript.CdsOneBasedStart;
// We may have to calculate 'netCdsChange', which is the effect on the CDS
NetCodingSequenceChange = NetCdsChange();
if (RequireNetCdsChange && NetCodingSequenceChange == "")
{ // This can happen on mixed changes where the 'InDel' part lies outside the transcript's exons
CodonsReference = "";
CodonsAlternate = "";
return;
}
//---
// Concatenate all exons
//---
int firstCdsBaseInExon = 0; // Where the exon maps to the CDS (i.e. which CDS base number does the first base in this exon maps to).
List <Exon> exons = Transcript.ExonsSortedStrand;
foreach (Exon exon in exons)
{
Exon = exon;
if (exon.Intersects(Variant))
{
long cdsBaseInExon; // cdsBaseInExon: base number relative to the beginning of the coding part of this exon (i.e. excluding 5'UTRs)
if (Transcript.IsStrandPlus())
{
long firstvariantBaseInExon = Math.Max(Variant.OneBasedStart, Math.Max(exon.OneBasedStart, cdsStart));
cdsBaseInExon = firstvariantBaseInExon - Math.Max(exon.OneBasedStart, cdsStart);
}
else
{
long lastvariantBaseInExon = Math.Min(Variant.OneBasedEnd, Math.Min(exon.OneBasedEnd, cdsStart));
cdsBaseInExon = Math.Min(exon.OneBasedEnd, cdsStart) - lastvariantBaseInExon;
}
if (cdsBaseInExon < 0)
{
cdsBaseInExon = 0;
}
// Get codon number and index within codon (where seqChage is pointing)
if (CodonStartNumber < 0)
{
CodonStartNumber = (int)(firstCdsBaseInExon + cdsBaseInExon) / CODON_SIZE;
CodonStartIndex = (int)(firstCdsBaseInExon + cdsBaseInExon) % CODON_SIZE;
}
// Use appropriate method to calculate codon change
bool hasChanged = false; // Was there any change?
hasChanged = ChangeCodon(exon); // This is overriden for the specific type of codon change
// Any change? => Add change to list
if (hasChanged && !VariantEffects.HasMarker())
{
VariantEffects.SetMarker(exon); // It is affecting this exon, so we set the marker
}
// Can we finish after effect of first exon is added?
if (ReturnNow)
{
return;
}
}
firstCdsBaseInExon += Transcript.IsStrandPlus() ?
(int)Math.Max(0, exon.OneBasedEnd - Math.Max(exon.OneBasedStart, cdsStart) + 1) :
(int)Math.Max(0, Math.Min(cdsStart, exon.OneBasedEnd) - exon.OneBasedStart + 1);
}
}
