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
});
}
}
