public void BasicReadTest()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr17", "17", 16), 41234419, "A");
var reader = new ClinVarXmlReader(new FileInfo(Resources.ClinvarXmlFiles("RCV000077146.xml")), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal("RCV000077146.3", clinVarItem.Id);
switch (clinVarItem.Id)
{
case "RCV000077146.3":
Assert.Equal("17", clinVarItem.Chromosome.EnsemblName);
Assert.Equal(41234419, clinVarItem.Start);
Assert.Equal("A", clinVarItem.ReferenceAllele);
Assert.Equal("C", clinVarItem.AlternateAllele);
Assert.Equal(ClinVarXmlReader.ParseDate("2016-07-31"), clinVarItem.LastUpdatedDate);
Assert.True(clinVarItem.AlleleOrigins.SequenceEqual(new List <string> {
"germline"
}));
Assert.Equal("C2676676", clinVarItem.MedGenIDs.First());
Assert.Equal("145", clinVarItem.OrphanetIDs.First());
Assert.Equal("604370", clinVarItem.OmimIDs.First());
Assert.Equal("Breast-ovarian cancer, familial 1", clinVarItem.Phenotypes.First());
Assert.Null(clinVarItem.PubmedIds);
break;
}
}
}
public void BasicReadTest()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000077146.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.Equal("RCV000077146.3", clinVarItem.ID);
switch (clinVarItem.ID)
{
case "RCV000077146.3":
Assert.Equal("17", clinVarItem.Chromosome);
Assert.Equal(41234419, clinVarItem.Start);
Assert.Equal("A", clinVarItem.ReferenceAllele);
Assert.Equal("C", clinVarItem.AltAllele);
Assert.Equal(ClinVarXmlReader.ParseDate("2016-07-31"), clinVarItem.LastUpdatedDate);
Assert.True(clinVarItem.AlleleOrigins.SequenceEqual(new List <string> {
"germline"
}));
Assert.Equal("C2676676", clinVarItem.MedGenIDs.First());
Assert.Equal("145", clinVarItem.OrphanetIDs.First());
Assert.Equal("604370", clinVarItem.OmimIDs.First());
Assert.Equal("Breast-ovarian cancer, familial 1", clinVarItem.Phenotypes.First());
Assert.Null(clinVarItem.PubmedIds);
break;
}
}
}
public void IndelTest()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000032548.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.Equal("RCV000032548.5", clinVarItem.ID);
switch (clinVarItem.ID)
{
case "RCV000032548.5":
Assert.Equal("4", clinVarItem.Chromosome);
Assert.Equal(187122303, clinVarItem.Start);
Assert.Equal(17, clinVarItem.ReferenceAllele.Length);
Assert.Equal("GC", clinVarItem.AltAllele);
Assert.Equal(ClinVarXmlReader.ParseDate("2016-08-29"), clinVarItem.LastUpdatedDate);
break;
}
}
}
public void MultiEntryXmlParsing()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("MultiClinvar.xml")), _reader, _sequence);
var clinvarList = new List <ClinVarItem>();
foreach (var clinVarItem in reader)
{
switch (clinVarItem.ID)
{
case "RCV000000064.5":
Assert.Equal(ClinVarXmlReader.ParseDate("2016-02-17"), clinVarItem.LastUpdatedDate);
Assert.Equal("risk factor", clinVarItem.Significance);
break;
case "RCV000000068.3":
Assert.Equal(ClinVarXmlReader.ParseDate("2016-02-17"), clinVarItem.LastUpdatedDate);
Assert.Equal("pathogenic", clinVarItem.Significance);
Assert.Equal("C3150419", clinVarItem.MedGenIDs.First());
break;
case "RCV000000069.3":
Assert.Equal(ClinVarXmlReader.ParseDate("2016-02-17"), clinVarItem.LastUpdatedDate);
Assert.Equal("pathogenic", clinVarItem.Significance);
Assert.Equal("C3150419", clinVarItem.MedGenIDs.First());
Assert.Equal(20179356, clinVarItem.PubmedIds.First());
break;
default:
throw new InvalidDataException("Unexpected clinvar id encountered");
}
clinvarList.Add(clinVarItem);
}
clinvarList.Sort();
Assert.Equal(2, clinvarList.Count);
Assert.Equal("2", clinvarList[0].Chromosome);
Assert.Equal("22", clinvarList[1].Chromosome);
}
public void IndelTest()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr4", "4", 3), 187122303, "ACGTACGTACGTACGTA");
var reader = new ClinVarXmlReader(new FileInfo(Resources.ClinvarXmlFiles("RCV000032548.xml")), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal("RCV000032548.5", clinVarItem.Id);
switch (clinVarItem.Id)
{
case "RCV000032548.5":
Assert.Equal("4", clinVarItem.Chromosome.EnsemblName);
Assert.Equal(187122303, clinVarItem.Start);
Assert.Equal(17, clinVarItem.ReferenceAllele.Length);
Assert.Equal("GC", clinVarItem.AlternateAllele);
Assert.Equal(ClinVarXmlReader.ParseDate("2016-08-29"), clinVarItem.LastUpdatedDate);
break;
}
}
}