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 NonEnglishChars()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr1", "1", 0), 225592188, "TAGAAGA");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000087262.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal("Pelger-Huët anomaly", clinVarItem.Phenotypes.First());
}
}
public void MissingClinvarInsertion()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr1", "1", 1), 2337967, "G");
var reader = new ClinVarXmlReader(new FileInfo(Resources.ClinvarXmlFiles("RCV000179026.xml")), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(2337968, clinVarItem.Start);
}
}
public void MissingClinvarInsertionShift2()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr1", "1", 1), 9324412, "C");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000017510.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(9324413, clinVarItem.Position);
}
}
public void PubmedTest5()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr16", "16", 6), 88907409, "A");
var reader = new ClinVarXmlReader(new FileInfo(Resources.ClinvarXmlFiles("RCV000000734.xml")), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Null(clinVarItem.PubmedIds);
}
}
public void AlternatePhenotype()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr7", "7", 1), 42018228, "TC");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000032707.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.NotNull(clinVarItem.Phenotypes);
}
}
public void OmitOmimFromAltPhenotypes()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr1", "1", 1), 55529187, "G");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000030349.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Single(clinVarItem.OmimIds);
}
}
public void ClinvarInsertion()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chrX", "X", 1), 122318386, "A");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000153339.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(122318387, clinVarItem.Position);
}
}
public void TrimSpaceFromOmimIds()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chrX", "X", 1), 129283520, "A");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000373191.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Single(clinVarItem.OmimIds);
Assert.Equal("609060", clinVarItem.OmimIds.FirstOrDefault());
}
}
public void MissingAltAllele()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr1", "1", 0), 118165691, "C");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000120902.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal("C", clinVarItem.RefAllele);
Assert.Equal("G", clinVarItem.AltAllele);
}
}
public void PubmedTest5()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr16", "16", 6), 88907409, "A");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000000734.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(699, clinVarItem.VariationId);
Assert.Null(clinVarItem.PubmedIds);
Assert.Contains("\"variationId\":699", clinVarItem.GetJsonString());
}
}
public void PubmedTest4()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr10", "10", 6), 43609944, "GCTGT");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000021819.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(new List <long> {
7595167, 8099202, 8612479
}, clinVarItem.PubmedIds);
}
}
public void PubmedTest3()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr7", "7", 6), 55259485, "C");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000038438.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(new List <long> {
17285735, 17877814, 22848293, 24033266
}, clinVarItem.PubmedIds);
}
}
public void PubmedTest2()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr11", "11", 10), 5247993, "AAAG");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000016673.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(new List <long> {
6826539, 9113933, 9845707, 12000828, 12383672
}, clinVarItem.PubmedIds);
}
}
public void PubmedTest1()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr3", "3", 2), 10183457, "CGCACGCAGCTCCGCCCCGCG");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000152657.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(new List <long> {
12114475, 18836774, 22357542, 24033266
}, clinVarItem.PubmedIds);
}
}
public void CapturePhenotypicSeriesOmimIDandUniq()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr4", "4", 1), 122746325, "A");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000401212.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(clinVarItem.OmimIds, new List <string> {
"209900"
});
}
}
public void MultipleOrigins()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chrX", "X", 23), 18671566, "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 ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000080071.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
var expectedOrigins = new List <string> {
"germline", "maternal", "unknown"
};
Assert.Equal(expectedOrigins, clinVarItem.AlleleOrigins);
}
}
public void PubmedTest6()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr1", "1", 6), 118165691, "C");
//extracting from SCV record
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000120902.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(clinVarItem.PubmedIds, new List <long> {
24728327
});
}
}
public void CaptureGeneOmimId()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr4", "4", 1), 3494837, "TGCC");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000235027.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(clinVarItem.OmimIds, new List <string> {
"601462", "610285.0001"
});
}
}
public void CapturePhenotypeSeriesOmimId()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr4", "4", 1), 15513014, "GAA");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000406351.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(clinVarItem.OmimIds, new List <string> {
"213300"
});
}
}
public void Remove9DigitsPubmedId()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr11", "11", 1), 534286, "C");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000207504.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(clinVarItem.PubmedIds, new List <long> {
16329078, 16372351, 19213030, 21438134, 25741868
});
}
}
public void MultiScvPubmeds()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr7", "7", 3), 116411990, "C");
//extracting from SCV record
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000203290.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.Equal(clinVarItem.PubmedIds, new List <long> {
23806086, 24088041, 25736269
});
}
}
public void MultiScvPubmed()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr4", "4", 6), 15589553, "G");
//extracting from SCV record
var reader = new ClinVarXmlReader(new FileInfo(Resources.ClinvarXmlFiles("RCV000194003.xml")), sequenceProvider);
Assert.True(reader.GetItems().Any());
foreach (var clinVarItem in reader.GetItems())
{
Assert.True(clinVarItem.PubmedIds.SequenceEqual(new List <long> {
25741868, 26092869
}));
}
}
public void IupacBases()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr13", "13", 1), 32913457, "C");
var reader = new ClinVarXmlReader(new FileInfo(Resources.ClinvarXmlFiles("RCV000113363.xml")), sequenceProvider);
Assert.True(reader.GetItems().Any());
var altAlleles = new List <string>();
foreach (var clinVarItem in reader.GetItems())
{
altAlleles.Add(clinVarItem.AlternateAllele);
}
Assert.Equal(2, altAlleles.Count);
}
public void Skip_entries_with_inconsistant_start_end()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr9", "9", 1), 132903739, "AAACGCTCATAGAGTAACTGGTTGTGCAGTAAAAGCAACTGGTCTCAAACGCTCATAGAGTAACTGGTTGTGCAGTAAAAGCAACTGGTCTC");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000342164.xml"), sequenceProvider);
Assert.False(reader.GetItems().Any());
}
public void IupacBases()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh38, new Chromosome("chr13", "13", 1), 32339320, "C");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000113363.xml"), sequenceProvider);
Assert.True(reader.GetItems().Any());
var altAlleles = new List <string>();
foreach (var clinVarItem in reader.GetItems())
{
altAlleles.Add(clinVarItem.AltAllele);
Assert.Equal(new[] { "pathogenic" }, clinVarItem.Significances);
}
Assert.Equal(2, altAlleles.Count);
}
public void SkipMicrosatellitesWithoutAltAllele()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr22", "22", 1), 46191240, "ATTCT");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000001054.xml"), sequenceProvider);
Assert.False(reader.GetItems().Any());
}
public void RCV000435546_NotMissing()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr12", "12", 11), 110221557, "CGCGG");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000435546.xml"), sequenceProvider);
var clinVarItems = reader.GetItems();
Assert.True(clinVarItems.Any());
}
public void RemoveDuplicationWithWrongRefSequence()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr3", "3", 1), 10183702, "GCGGCCGCGGCCCG");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000267121.xml"), sequenceProvider);
Assert.False(reader.GetItems().Any());
}
public void SkipMicrosattelite()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr16", "16", 15), 87637894, "CTG");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000005426.xml"), sequenceProvider);
Assert.False(reader.GetItems().Any());
}