public static UgaGene Merge(UgaGene gene37, UgaGene gene38)
{
string ensemblId = CombineField(gene37.EnsemblId, gene38.EnsemblId);
string entrezGeneId = CombineField(gene37.EntrezGeneId, gene38.EntrezGeneId);
int hgncId = CombineField(gene37.HgncId, gene38.HgncId);
return(new UgaGene(gene37.Chromosome, gene37.GRCh37, gene38.GRCh38, gene37.OnReverseStrand, entrezGeneId,
ensemblId, gene37.Symbol, hgncId));
}
public void Merge_DifferentCombinations()
{
var interval = new Interval(17369, 17436);
var uga37 = new UgaGene(ChromosomeUtilities.Chr1, interval, null, true, "102466751", null, "MIR6859-1", 50039);
var uga38 = new UgaGene(ChromosomeUtilities.Chr1, null, interval, true, null, "ENSG00000278267", "MIR6859-1", 50039);
var observedResult = CombinerUtils.Merge(uga37, uga38);
Assert.Equal("102466751", observedResult.EntrezGeneId);
Assert.Equal("ENSG00000278267", observedResult.EnsemblId);
}
public void Merge_ThrowException_IfValuesDifferent()
{
var interval = new Interval(17369, 17436);
var uga37 = new UgaGene(ChromosomeUtilities.Chr1, interval, null, true, "102466751", "ENSG00000278267", "MIR6859-1", 50039);
var uga38 = new UgaGene(ChromosomeUtilities.Chr1, null, interval, true, "000000000", "ENSG00000278267", "MIR6859-1", 50039);
Assert.Throws <InvalidDataException>(delegate
{
// ReSharper disable once UnusedVariable
var observedResult = CombinerUtils.Merge(uga37, uga38);
});
}
public void GetSingleValueDict_ThrowException_IfMultipleValuesShareKey()
{
var uga1 = new UgaGene(null, null, null, true, null, "ENSG00000278267", "MIR6859-1", 50039);
var uga2 = new UgaGene(null, null, null, true, null, "ENSG00000278267", "MIR6859-1", 50039);
var genes = new List <UgaGene> {
uga1, uga2
};
Assert.Throws <InvalidDataException>(delegate
{
// ReSharper disable once UnusedVariable
var observedResult = genes.GetSingleValueDict(x => x.EnsemblId);
});
}
public void GetSingleValueDict_OneKey_OneValue()
{
var uga1 = new UgaGene(null, null, null, true, "102466751", null, "MIR6859-1", 50039);
var uga2 = new UgaGene(null, null, null, true, null, "ENSG00000278267", "MIR6859-1", 50039);
var genes = new List <UgaGene> {
uga1, uga2
};
var observedResult = genes.GetSingleValueDict(x => x.EnsemblId);
Assert.NotNull(observedResult);
Assert.Single(observedResult);
Assert.True(observedResult.ContainsKey("ENSG00000278267"));
}
private static bool UpdateBySymbolDict <T>(UgaGene gene, Func <UgaGene, T> idFunc, Func <T, bool> isEmpty, IReadOnlyDictionary <T, string> idToSymbol)
{
var key = idFunc(gene);
if (isEmpty(key))
{
return(false);
}
if (!idToSymbol.TryGetValue(idFunc(gene), out string symbol))
{
return(false);
}
gene.Symbol = symbol;
return(true);
}
public void GetKeyValueDict_OneKey_OneValue()
{
var uga1 = new UgaGene(null, null, null, true, "102466751", null, "MIR6859-1", 50039);
var uga2 = new UgaGene(null, null, null, true, null, "ENSG00000278267", "MIR6859-1", 50039);
var uga3 = new UgaGene(null, null, null, true, null, "ENSG00000278267", "MIR6859-1", 50039);
var genes = new List <UgaGene> {
uga1, uga2, uga3
};
var observedResult = genes.GetKeyValueDict(x => x.EnsemblId, x => x.HgncId);
Assert.NotNull(observedResult);
Assert.Single(observedResult);
var hgncId = observedResult["ENSG00000278267"];
Assert.Equal(50039, hgncId);
}
private void UpdateGeneSymbol(UgaGene gene)
{
string originalSymbol = gene.Symbol;
bool isUpdated = UpdateBySymbolDict(gene, x => x.HgncId, x => x == -1, _hgncIdToSymbol);
if (isUpdated)
{
if (gene.Symbol != originalSymbol)
{
_numUpdatedByHgncId++;
}
return;
}
isUpdated = UpdateBySymbolDict(gene, x => x.EntrezGeneId, string.IsNullOrEmpty, _entrezGeneIdToSymbol);
if (isUpdated)
{
if (gene.Symbol != originalSymbol)
{
_numUpdatedByEntrezGeneId++;
}
return;
}
isUpdated = UpdateBySymbolDict(gene, x => x.EnsemblId, string.IsNullOrEmpty, _ensemblIdToSymbol);
if (isUpdated)
{
if (gene.Symbol != originalSymbol)
{
_numUpdatedByEnsemblId++;
}
return;
}
isUpdated = UpdateBySymbolDict(gene, x => x.EntrezGeneId, string.IsNullOrEmpty, _refseqGeneIdToSymbol);
// ReSharper disable once InvertIf
if (isUpdated && gene.Symbol != originalSymbol)
{
_numUpdatedByRefSeqGff++;
}
}
public void GetMultiValueDict_OneKey_WithTwoValues()
{
var uga1 = new UgaGene(null, null, null, true, "102466751", null, "MIR6859-1", 50039);
var uga2 = new UgaGene(null, null, null, true, null, "ENSG00000278267", "MIR6859-1", 50039);
var uga3 = new UgaGene(null, null, null, true, null, "ENSG00000278267", "MIR6859-1", 50039);
var genes = new List <UgaGene> {
uga1, uga2, uga3
};
var observedResult = genes.GetMultiValueDict(x => x.EnsemblId);
Assert.NotNull(observedResult);
Assert.Single(observedResult);
var firstEntry = observedResult["ENSG00000278267"];
Assert.NotNull(firstEntry);
Assert.Equal(2, firstEntry.Count);
}
private static string GetKey(UgaGene gene) => gene.EnsemblId + '|' + gene.EntrezGeneId + '|' + (gene.OnReverseStrand ? "R" : "F");
private static int MinCoordinate(UgaGene gene, Func <IInterval, int> coordFunc) => coordFunc(gene.GRCh37 ?? gene.GRCh38);
