public void MergeDbSnpClinVar()
{
const string vcfLine = "1 225592188 rs387906416 TAGAAGA CTTCTAG . . RS=387906416;RSPOS=225592188;RV;dbSNPBuildID=137;SSR=0;SAO=1;VP=0x050060000605000002110800;GENEINFO=LBR:3930;WGT=1;VC=MNV;PM;NSN;REF;ASP;LSD;OM";
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItems = dbsnpReader.ExtractItem(vcfLine);
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(225592188));
foreach (var dbSnpItem in dbSnpItems)
{
dbSnpItem.SetSupplementaryAnnotations(sa);
}
var xmlReader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000087262.xml")), _reader, _sequence);
foreach (var clinVarItem in xmlReader)
{
var sa1 = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(225592188));
clinVarItem.SetSupplementaryAnnotations(sa1);
sa.MergeSaCreator(sa1);
}
Assert.Equal(1, sa.SaPosition.ClinVarItems.Count);
foreach (var clinVarEntry in sa.SaPosition.ClinVarItems)
{
Assert.Equal(clinVarEntry.ID, "RCV000087262.3");
Assert.Equal(clinVarEntry.MedGenIDs.First(), "C0030779");
Assert.Equal(clinVarEntry.Phenotypes.First(), "Pelger-Huët anomaly");
}
}
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 MultiVariantEntry()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000007484.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
switch (clinVarItem.Start)
{
case 8045031:
Assert.Equal("G", clinVarItem.ReferenceAllele);
Assert.Equal("A", clinVarItem.AltAllele);
break;
case 8021911:
Assert.Equal("GTGCTGGACGGTGTCCCT", clinVarItem.AltAllele);
var sa = new SupplementaryAnnotationPosition(clinVarItem.Start);
var saCreator = new SupplementaryPositionCreator(sa);
clinVarItem.SetSupplementaryAnnotations(saCreator);
Assert.Equal("iGTGCTGGACGGTGTCCCT", clinVarItem.SaAltAllele);
break;
default:
throw new InvalidDataException($"Unexpected clinvar item start point : {clinVarItem.Start}");
}
}
}
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 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 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 EmptyRefAndAlt()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr2", "2", 3), 31805881, "G");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000083638.xml"), sequenceProvider);
Assert.False(reader.GetItems().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 Discard_entries_with_unknown_variant_type()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chrX", "X", 0), 66765160, "CAG");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000485802.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());
}
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 MissingClinvarInsertionShift2()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000017510.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.Equal(9324413, clinVarItem.Start);
}
}
public void NoClinVarItem_due_to_ref_mismatch()
{
var sequenceProvider =
GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr10", "10", 10), 90982267, "A");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000000101.xml"), sequenceProvider);
Assert.False(reader.GetItems().Any());
}
public void PubmedTest5()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000000734.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.Null(clinVarItem.PubmedIds);
}
}
public void ClinvarInsertion()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000153339.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.Equal(122318387, clinVarItem.Start);
}
}
public void OmitOmimFromAltPhenotypes()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000030349.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.Equal(1, clinVarItem.OmimIDs.Count());
}
}
public void AlternatePhenotype()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000032707.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.NotNull(clinVarItem.Phenotypes);
}
}
public void SkipMicrosattelite()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000005426.xml")), _reader, _sequence);
var clinvarItems = reader.GetEnumerator();
Assert.Null(clinvarItems.Current);
clinvarItems.Dispose();
}
public void EmptyRefAndAlt()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000083638.xml")), _reader, _sequence);
var clinvarItems = reader.GetEnumerator();
Assert.Null(clinvarItems.Current);
clinvarItems.Dispose();
}
public void Multiple_significance_from_explanation()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh38, new Chromosome("chr19", "19", 19), 12665750, "T");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000001752.xml"), sequenceProvider);
var clinvarItems = reader.GetItems().ToList();
Assert.Equal(new[] { "pathogenic", "uncertain significance" }, clinvarItems[0].Significances);
}
public void Mising_entry()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr13", "13", 12), 36888396, "C");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000171474.xml"), sequenceProvider);
var clinvarItems = reader.GetItems().ToList();
Assert.Equal("", clinvarItems[0].RefAllele);
}
public void Multiple_significance()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh38, new Chromosome("chr15", "15", 15), 72349076, "T");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000169296.xml"), sequenceProvider);
var clinvarItems = reader.GetItems().ToList();
Assert.Equal(new[] { "pathogenic", "likely pathogenic" }, clinvarItems[0].Significances);
}
public void MissingClinvarInsertion2()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh38, new Chromosome("chr9", "9", 1), 132903739, "AAACGCTCATAGAGTAACTGGTTGTGCAGTAAAAGCAACTGGTCTCAAACGCTCATAGAGTAACTGGTTGTGCAGTAAAAGCAACTGGTCTC");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000342164.xml"), sequenceProvider);
var clinvarItems = reader.GetItems().ToList();
Assert.Single(clinvarItems);
}
public void Alternate_phenotypes()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr2", "2", 1), 204732740, "G");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000537563.xml"), sequenceProvider);
var clinvarItems = reader.GetItems().ToList();
Assert.Single(clinvarItems[0].Phenotypes);
}
public void NonEnglishChars()
{
//NIR-900
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000087262.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.Equal("Pelger-Huët anomaly", clinVarItem.Phenotypes.First());
}
}
public void MultipleEntryRecordVariant2()
{
var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, new Chromosome("chr1", "1", 1), 8021910, "ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT");
var reader = new ClinVarXmlReader(Resources.ClinvarXmlFiles("RCV000007484.xml"), sequenceProvider);
var clinvarItems = reader.GetItems().ToList();
Assert.Single(clinvarItems);
}
public void MissingAltAllele()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000120902.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.Equal("C", clinVarItem.ReferenceAllele);
Assert.Equal("G", clinVarItem.AltAllele);
}
}
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 PubmedTest4()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000021819.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.True(clinVarItem.PubmedIds.SequenceEqual(new List <long> {
8099202
}));
}
}
public void Remove9DigitsPubmedId()
{
var reader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000207504.xml")), _reader, _sequence);
foreach (var clinVarItem in reader)
{
Assert.True(clinVarItem.PubmedIds.SequenceEqual(new List <long> {
16329078, 16372351, 19213030, 21438134, 25741868
}));
}
}
