public void Parse_deletions()
{
using (var spliceParser = new SpliceAiParser(GetDeletionStream(), GetSequenceProvider(), GetSpliceIntervals(), GetSpliceToNirvanaGenes()))
{
var spliceItems = spliceParser.GetItems().ToList();
Assert.Equal(3, spliceItems.Count);
}
}
public void Check_position_caching()
{
using (var spliceParser = new SpliceAiParser(GetPositionCachingStream(), GetSequenceProvider(), GetSpliceIntervals(), GetSpliceToNirvanaGenes()))
{
var spliceItems = spliceParser.GetItems().ToList();
Assert.Equal(5, spliceItems.Count);
}
}
public void Parse_multiScore_entry()
{
using (var spliceParser = new SpliceAiParser(GetMultiScoreStream(), GetSequenceProvider(), GetSpliceIntervals(), GetSpliceToNirvanaGenes()))
{
var spliceItems = spliceParser.GetItems().ToList();
Assert.Single(spliceItems);
Assert.Equal("\"hgnc\":\"TUBB8\",\"acceptorGainScore\":0.2,\"acceptorGainDistance\":-7,\"acceptorLossScore\":0.4,\"acceptorLossDistance\":-50,\"donorGainScore\":0,\"donorGainDistance\":-7,\"donorLossScore\":0.2,\"donorLossDistance\":-6", spliceItems[0].GetJsonString());
}
}
public void Skip_shiftable_indels()
{
using (var spliceParser = new SpliceAiParser(GetShiftableInsertionStream(), GetSequenceProvider(), GetSpliceIntervals(), GetSpliceToNirvanaGenes()))
{
var spliceItems = spliceParser.GetItems().ToList();
Assert.Single(spliceItems);
Assert.Equal("\"hgnc\":\"CECR5\",\"acceptorGainScore\":0.1,\"acceptorGainDistance\":-10", spliceItems[0].GetJsonString());
}
}
public void MissingEntry()
{
using (var spliceParser = new SpliceAiParser(GetMissingEntryStream(), GetSequenceProvider(), GetSpliceIntervals(), GetSpliceToNirvanaGenes()))
{
var spliceItems = spliceParser.GetItems().ToList();
Assert.Equal(2, spliceItems.Count);
Assert.Equal("\"hgnc\":\"AP000304.12\",\"acceptorGainScore\":0.1,\"acceptorGainDistance\":-12,\"acceptorLossScore\":0,\"acceptorLossDistance\":24,\"donorGainScore\":0,\"donorGainDistance\":-41,\"donorLossScore\":0,\"donorLossDistance\":5", spliceItems[0].GetJsonString());
}
}
public void Two_symbols_in_spliceAi()
{
using (var spliceParser = new SpliceAiParser(GetMultiGeneAtSameLocationStream(), GetSequenceProvider(), GetSpliceIntervals(), GetSpliceToNirvanaGenes()))
{
var spliceItems = spliceParser.GetItems().ToList();
Assert.Equal(2, spliceItems.Count);
Assert.Equal("\"hgnc\":\"KRTAP19-3\",\"acceptorGainScore\":0,\"acceptorGainDistance\":-42,\"acceptorLossScore\":0,\"acceptorLossDistance\":38,\"donorGainScore\":0,\"donorGainDistance\":23,\"donorLossScore\":0,\"donorLossDistance\":38", spliceItems[0].GetJsonString());
Assert.Equal("\"hgnc\":\"KRTAP19-2\",\"acceptorGainScore\":0,\"acceptorGainDistance\":-42,\"acceptorLossScore\":0,\"acceptorLossDistance\":38,\"donorGainScore\":0,\"donorGainDistance\":23,\"donorLossScore\":0,\"donorLossDistance\":-11", spliceItems[1].GetJsonString());
}
}
public void Parse_multiGene_entry()
{
using (var spliceParser = new SpliceAiParser(GetMultiGeneStream(), GetSequenceProvider(), GetSpliceIntervals(), GetSpliceToNirvanaGenes()))
{
var spliceItems = spliceParser.GetItems().ToList();
Assert.Equal(2, spliceItems.Count);
Assert.Equal("\"hgnc\":\"MMP23B\",\"acceptorGainScore\":0,\"acceptorGainDistance\":8,\"acceptorLossScore\":0,\"acceptorLossDistance\":-16,\"donorGainScore\":0,\"donorGainDistance\":-16,\"donorLossScore\":0,\"donorLossDistance\":26", spliceItems[0].GetJsonString());
Assert.Equal("\"hgnc\":\"CDK11B\",\"acceptorGainScore\":0.9,\"acceptorGainDistance\":-2,\"acceptorLossScore\":0,\"acceptorLossDistance\":-8,\"donorGainScore\":0,\"donorGainDistance\":33,\"donorLossScore\":0,\"donorLossDistance\":-13", spliceItems[1].GetJsonString());
}
}
public void Parse_standard_lines()
{
using (var spliceParser = new SpliceAiParser(GetStream(), GetSequenceProvider(), GetSpliceIntervals(), GetSpliceToNirvanaGenes()))
{
var spliceItems = spliceParser.GetItems().ToList();
Assert.Equal(3, spliceItems.Count);
Assert.Equal("\"hgnc\":\"TUBB8\",\"acceptorGainScore\":0,\"acceptorGainDistance\":-26,\"acceptorLossScore\":0,\"acceptorLossDistance\":-10,\"donorGainScore\":0,\"donorGainDistance\":3,\"donorLossScore\":0,\"donorLossDistance\":35", spliceItems[0].GetJsonString());
Assert.Equal("\"hgnc\":\"TUBB8\",\"acceptorGainScore\":0.1,\"acceptorGainDistance\":-11", spliceItems[1].GetJsonString());
Assert.Equal("\"hgnc\":\"TUBB8\",\"acceptorGainScore\":0.2,\"acceptorGainDistance\":-7,\"acceptorLossScore\":0,\"acceptorLossDistance\":-50,\"donorGainScore\":0,\"donorGainDistance\":-7,\"donorLossScore\":0,\"donorLossDistance\":-6", spliceItems[2].GetJsonString());
}
}
public void Check_multi_chromosome_gene_update()
{
using (var spliceParser = new SpliceAiParser(GetMultiChromosomeStream(), GetSequenceProvider(), GetSpliceIntervals(), GetGeneForest(), GetGeneSymbolSynonyms()))
{
var spliceItems = spliceParser.GetItems().ToList();
Assert.Equal(3, spliceItems.Count);
Assert.Equal("GENE1", spliceItems[0].Hgnc);
Assert.Equal("GENE8", spliceItems[1].Hgnc);
Assert.Null(spliceItems[2].Hgnc);
}
}
public void Check_multi_chromosome_gene_update()
{
using (var spliceParser = new SpliceAiParser(GetMultiChromosomeStream(), GetSequenceProvider(), GetSpliceIntervals(), GetSpliceToNirvanaGenes()))
{
var spliceItems = spliceParser.GetItems().ToList();
// the third item will be skipped since hgnc is null
Assert.Equal(3, spliceItems.Count);
Assert.Equal("TUBB8", spliceItems[0].Hgnc);
//checking a case where the splice AI gene is different from Nirvana
Assert.Equal("NIR91", spliceItems[1].Hgnc);
}
}