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}"); } } }