public void NoClinVarItem_due_to_ref_mismatch() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 90982267, "A"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000000101.xml")), Stream.Null, sequenceProvider); Assert.False(reader.GetRcvItems().Any()); }
public void Alternate_phenotypes() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 204732740, "G"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000537563.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems().ToList(); Assert.Single(clinvarItems[0].Phenotypes); }
public void MissingClinvarInsertion2() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh38, 132903738, "A"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000342164.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems().ToList(); Assert.Single(clinvarItems); }
public void Mising_entry() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 36888396, "C"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000171474.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems().ToList(); Assert.Equal("", clinvarItems[0].RefAllele); }
public void Multiple_significance() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh38, 72349076, "T"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000169296.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems().ToList(); Assert.Equal(new[] { "pathogenic", "likely pathogenic" }, clinvarItems[0].Significances); }
public void Multiple_significance_from_explanation() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh38, 12665750, "T"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000001752.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems().ToList(); Assert.Equal(new[] { "pathogenic", "uncertain significance" }, clinvarItems[0].Significances); }
public void Override_microsatellite_type() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 88929173, "CGAG"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000205418.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems(); Assert.Single(clinvarItems); }
public void MultipleEntryRecordVariant2() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 8021910, "G"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000007484.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems().ToList(); Assert.Single(clinvarItems); }
public void OneRcv_oneVcv() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 31496350, "C"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000124712.xml")), FileUtilities.GetReadStream(Resources.VcvXmlFiles("VCV000137106.xml")), sequenceProvider); var items = reader.GetItems().ToArray(); Assert.Equal(2, items.Length); }
public void OmitOmimFromAltPhenotypes() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 55529187, "G"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000030349.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Single(clinVarItem.OmimIds); } }
public void MissingClinvarInsertionShift2() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 9324412, "C"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000017510.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(9324413, clinVarItem.Position); } }
public void AlternatePhenotype() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 42018227, "GTC"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000032707.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.NotNull(clinVarItem.Phenotypes); } }
public void NonEnglishChars() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 225592188, "TAGAAGA"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000087262.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal("Pelger-Huët anomaly", clinVarItem.Phenotypes.First()); } }
public void ClinvarInsertion() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 122318386, "A"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000153339.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(122318387, clinVarItem.Position); } }
public void TrimSpaceFromOmimIds() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 129283520, "A"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000373191.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Single(clinVarItem.OmimIds); Assert.Equal("609060", clinVarItem.OmimIds.FirstOrDefault()); } }
public void AllelicOmimIdsForDeletions() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 111335401, "GCTC"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000170338.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems().ToList(); Assert.Single(clinvarItems); var clinvarItem = clinvarItems[0]; Assert.Single(clinvarItem.OmimIds); Assert.Equal("612800.0002", clinvarItem.OmimIds.First()); }
public void MissingAltAllele() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 118165691, "C"); 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("C", clinVarItem.RefAllele); Assert.Equal("G", clinVarItem.AltAllele); } }
public void AllelicOmimIdsFromAttributeSetChrY() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 545469, "C"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000010551.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems().ToList(); Assert.Single(clinvarItems); foreach (var clinVarItem in clinvarItems) { Assert.Equal(2, clinVarItem.OmimIds.Count()); } }
public void ExcludeAllelicOmimIdsFromTraits() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 100887648, "AGAT"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000050055.xml")), Stream.Null, sequenceProvider); var clinvarItems = reader.GetRcvItems().ToList(); Assert.Single(clinvarItems); var clinvarItem = clinvarItems[0]; Assert.Single(clinvarItem.OmimIds); Assert.Equal("216550", clinvarItem.OmimIds.First()); }
public void ClinVarForRef() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 31496350, "C"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000124712.xml")), Stream.Null, sequenceProvider); var clinVarList = new List <ClinVarItem>(); foreach (var clinVarItem in reader.GetRcvItems()) { clinVarList.Add(clinVarItem); Assert.Equal(clinVarItem.RefAllele, clinVarItem.AltAllele); } Assert.Single(clinVarList); }
public void CapturePhenotypeSeriesOmimId() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 15513004, "GGAA"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000406351.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(clinVarItem.OmimIds, new List <string> { "213300" }); } }
public void CaptureGeneOmimId() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 3494833, "A"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000235027.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(clinVarItem.OmimIds, new List <string> { "601462", "610285.0001" }); } }
public void Remove9DigitsPubmedId() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 534286, "C"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000207504.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(clinVarItem.PubmedIds, new List <long> { 16329078, 16372351, 19213030, 21438134, 25741868 }); } }
public void PubmedTest1() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 10183453, "AGCGCGCACGCAGCTCCGCCCC"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000152657.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(new List <long> { 12114475, 18836774, 22357542, 24033266 }, clinVarItem.PubmedIds); } }
public void PubmedTest2() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 5247992, "CAAAG"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000016673.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(new List <long> { 6826539, 9113933, 9845707, 12000828, 12383672 }, clinVarItem.PubmedIds); } }
public void PubmedTest3() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 55259485, "C"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000038438.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(new List <long> { 17285735, 17877814, 22848293, 24033266 }, clinVarItem.PubmedIds); } }
public void PubmedTest4() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 43609944, "GCTGT"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000021819.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(new List <long> { 7595167, 8099202, 8612479 }, clinVarItem.PubmedIds); } }
public void PubmedTest5() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 88907409, "A"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000000734.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(699, clinVarItem.VariationId); Assert.Null(clinVarItem.PubmedIds); Assert.Contains("\"variationId\":699", clinVarItem.GetJsonString()); } }
public void RCV000001373_NoExtraOmimId() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 3209662, "AGCAGACGGGCA"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000001373.xml")), Stream.Null, sequenceProvider); var clinVarItems = reader.GetRcvItems().ToArray(); Assert.Single(clinVarItems); var clinVarItem = clinVarItems[0]; Assert.Equal("RCV000001373.3", clinVarItem.Id); var omimIds = clinVarItem.OmimIds; Assert.Single(omimIds); Assert.Equal("610206.0007", omimIds.First()); }
public void MultiScvPubmeds() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 116411990, "C"); //extracting from SCV record var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000203290.xml")), Stream.Null, sequenceProvider); var items = reader.GetRcvItems(); Assert.True(items.Any()); foreach (var clinVarItem in items) { Assert.Equal(clinVarItem.PubmedIds, new List <long> { 23806086, 24088041, 25736269 }); } }