public void MultiScvPubmed()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 15589551, "AG");
//extracting from SCV record
var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000194003.xml")), Stream.Null, sequenceProvider);
var items = reader.GetRcvItems();
Assert.True(items.Any());
foreach (var clinVarItem in items)
{
Assert.Equal(clinVarItem.PubmedIds, new List <long> {
25741868, 26092869
});
}
}
public void PubmedTest7_comma_trimming()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 41258568, "A");
//extracting from SCV record
var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000167792.xml")), Stream.Null, sequenceProvider);
var items = reader.GetRcvItems();
Assert.True(items.Any());
foreach (var clinVarItem in items)
{
Assert.Equal(clinVarItem.PubmedIds, new List <long> {
23239986, 28492532, 30472649
});
}
}
public void PubmedTest6()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 118165691, "C");
//extracting from SCV record
var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000120902.xml")), Stream.Null, sequenceProvider);
var items = reader.GetRcvItems();
Assert.True(items.Any());
foreach (var clinVarItem in items)
{
Assert.Equal(clinVarItem.PubmedIds, new List <long> {
24728327
});
}
}
public void MultiplePhenotypes()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 172659738, "C");
//no citations show up for this RCV in the website. But the XML has these pubmed ids under fields that we parse pubmed ids from
var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000144179.xml")), Stream.Null, sequenceProvider);
var items = reader.GetRcvItems();
Assert.True(items.Any());
foreach (var clinVarItem in items)
{
var expectedPhenotypes = new List <string> {
"Single ventricle", "small Atrial septal defect"
};
Assert.Equal(expectedPhenotypes, clinVarItem.Phenotypes);
}
}
public void IupacBases()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh38, 32339320, "C");
var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000113363.xml")), Stream.Null, sequenceProvider);
var items = reader.GetRcvItems();
Assert.True(items.Any());
var altAlleles = new List <string>();
foreach (var clinVarItem in items)
{
altAlleles.Add(clinVarItem.AltAllele);
Assert.Equal(new[] { "pathogenic" }, clinVarItem.Significances);
}
Assert.Equal(2, altAlleles.Count);
}
public void MultipleAlleleOrigins()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 32890572, "G");
var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000112977.xml")), Stream.Null, sequenceProvider);
var items = reader.GetRcvItems();
Assert.True(items.Any());
foreach (var clinVarItem in items)
{
Assert.Equal(2, clinVarItem.AlleleOrigins.Count());
Assert.NotEqual(clinVarItem.AlleleOrigins.First(), clinVarItem.AlleleOrigins.Last());
foreach (var origin in clinVarItem.AlleleOrigins)
{
Assert.True(origin == "unknown" || origin == "germline");
}
}
}
public void SkipGeneralCitations()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 67705958, "G");
//no citations show up for this RCV in the website. But the XML has these pubmed ids under fields that we parse pubmed ids from
var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000003254.xml")), Stream.Null, sequenceProvider);
foreach (var clinVarItem in reader.GetRcvItems())
{
Assert.Equal(clinVarItem.PubmedIds, new List <long>
{
12023369,
17068223,
17447842,
17587057,
17786191,
17804789,
18438406,
19122664,
20228799
});
}
}
public void WrongPosition()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 112064826, "G");
var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000073701.xml")), Stream.Null, sequenceProvider);
var items = reader.GetRcvItems();
Assert.True(items.Any());
foreach (var clinVarItem in items)
{
switch (clinVarItem.Position)
{
case 112064826:
Assert.Equal("G", clinVarItem.RefAllele);
Assert.Equal("C", clinVarItem.AltAllele);
break;
default:
throw new InvalidDataException($"Unexpected clinvar item start point : {clinVarItem.Position}");
}
}
}
