private static DataStructures.VEP.Transcript GetTranscript(BioType bioType, DataStructures.VEP.Transcript prev, DataStructures.VEP.Transcript curr)
{
if (prev.BioType == bioType)
{
return(prev);
}
if (curr.BioType == bioType)
{
return(curr);
}
return(null);
}
private static void FixCanonical(DataStructures.VEP.Transcript prev, DataStructures.VEP.Transcript curr)
{
if (prev.IsCanonical == curr.IsCanonical)
{
return;
}
if (!prev.IsCanonical)
{
prev.IsCanonical = true;
}
if (!curr.IsCanonical)
{
curr.IsCanonical = true;
}
}
private static void AddGeneSymbol(DataStructures.VEP.Transcript prev, DataStructures.VEP.Transcript curr)
{
var prevHasSymbol = string.IsNullOrEmpty(prev.GeneSymbol);
var currHasSymbol = string.IsNullOrEmpty(curr.GeneSymbol);
if (prevHasSymbol == currHasSymbol)
{
return;
}
if (!prevHasSymbol)
{
prev.GeneSymbol = curr.GeneSymbol;
}
if (!currHasSymbol)
{
curr.GeneSymbol = prev.GeneSymbol;
}
}
private static void MergeTranscript(DataStructures.VEP.Transcript prev, DataStructures.VEP.Transcript curr)
{
if (TranscriptEquals(prev, curr))
{
return;
}
AddGeneSymbol(prev, curr);
FixCanonical(prev, curr);
FixBiotype(prev, curr);
if (TranscriptEquals(prev, curr))
{
return;
}
TranscriptDump(prev);
TranscriptDump(curr);
throw new GeneralException("Found different transcripts");
}
private static bool TranscriptEquals(DataStructures.VEP.Transcript prev, DataStructures.VEP.Transcript curr)
{
return(prev.ReferenceIndex == curr.ReferenceIndex &&
prev.Start == curr.Start &&
prev.End == curr.End &&
prev.BioType == curr.BioType &&
prev.OnReverseStrand == curr.OnReverseStrand &&
prev.IsCanonical == curr.IsCanonical &&
prev.CompDnaCodingStart == curr.CompDnaCodingStart &&
prev.CompDnaCodingEnd == curr.CompDnaCodingEnd &&
prev.Version == curr.Version &&
prev.CcdsId == curr.CcdsId &&
prev.ProteinId == curr.ProteinId &&
prev.RefSeqId == curr.RefSeqId &&
prev.GeneStableId == curr.GeneStableId &&
prev.StableId == curr.StableId &&
prev.GeneSymbol == curr.GeneSymbol &&
prev.GeneSymbolSource == curr.GeneSymbolSource &&
prev.HgncId == curr.HgncId);
}
private static void FixBiotype(DataStructures.VEP.Transcript prev, DataStructures.VEP.Transcript curr)
{
if (prev.BioType == curr.BioType)
{
return;
}
var miRNA = GetTranscript(BioType.miRNA, prev, curr);
var rna = GetTranscript(BioType.RNA, prev, curr);
var mRNA = GetTranscript(BioType.mRNA, prev, curr);
var proteinCoding = GetTranscript(BioType.ProteinCoding, prev, curr);
var rRNA = GetTranscript(BioType.RibosomalRna, prev, curr);
// fix the miRNA vs misc_RNA issue
if (miRNA != null && rna != null)
{
rna.BioType = BioType.miRNA;
Console.WriteLine($"--- fixed biotype: miRNA vs misc_RNA: {curr.StableId}");
}
// fix the mRNA vs protein_coding issue
if (mRNA != null && proteinCoding != null)
{
mRNA.BioType = proteinCoding.BioType;
mRNA.TransExons = proteinCoding.TransExons;
mRNA.Translation = proteinCoding.Translation;
mRNA.VariantEffectCache = proteinCoding.VariantEffectCache;
mRNA.CompDnaCodingStart = proteinCoding.CompDnaCodingStart;
mRNA.CompDnaCodingEnd = proteinCoding.CompDnaCodingEnd;
mRNA.ProteinId = proteinCoding.ProteinId;
Console.WriteLine($"--- fixed biotype: mRNA vs protein_coding: {curr.StableId}");
}
// fix the misc_RNA vs rRNA issue
if (rna != null && rRNA != null)
{
rna.BioType = BioType.RibosomalRna;
Console.WriteLine($"--- fixed biotype: rRNA vs misc_RNA: {curr.StableId}");
}
}
private static void TranscriptDump(DataStructures.VEP.Transcript t)
{
Console.WriteLine("==================================");
Console.WriteLine($"ReferenceIndex: {t.ReferenceIndex}");
Console.WriteLine($"Start: {t.Start}");
Console.WriteLine($"End: {t.End}");
Console.WriteLine($"BioType: {BioTypeUtilities.GetBiotypeDescription(t.BioType)}");
Console.WriteLine($"OnReverseStrand: {t.OnReverseStrand}");
Console.WriteLine($"IsCanonical: {t.IsCanonical}");
Console.WriteLine($"CompDnaCodingStart: {t.CompDnaCodingStart}");
Console.WriteLine($"CompDnaCodingEnd: {t.CompDnaCodingEnd}");
Console.WriteLine($"Version: {t.Version}");
Console.WriteLine($"CcdsId: {t.CcdsId}");
Console.WriteLine($"DatabaseId: {t.DatabaseId}");
Console.WriteLine($"ProteinId: {t.ProteinId}");
Console.WriteLine($"RefSeqId: {t.RefSeqId}");
Console.WriteLine($"GeneStableId: {t.GeneStableId}");
Console.WriteLine($"StableId: {t.StableId}");
Console.WriteLine($"GeneSymbol: {t.GeneSymbol}");
Console.WriteLine($"GeneSymbolSource: {t.GeneSymbolSource}");
Console.WriteLine($"HgncId: {t.HgncId}");
Console.WriteLine("==================================");
}
