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; } } }