public void EndOfFileTest()
{
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(_randomPath))
{
var observedJumpAnnotation = reader.GetAnnotation(_expectedAnnotation3.ReferencePosition + 1);
Assert.Null(observedJumpAnnotation);
}
}
public void RwDbsnpGlobalAlleles()
{
//NIR-1262
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "147", DateTime.Parse("2016-07-26").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion
};
const string vcfLine1 =
"2 141724543 rs112783784 A C,T . . RS=112783784;RSPOS=141724543;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050100080015140136000100;WGT=1;VC=SNV;SLO;INT;OTH;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.04113,0.9105,0.04832;COMMON=1";
const string vcfLine2 =
"2 141724543 rs4300776 A C . . RS=4300776;RSPOS=141724543;dbSNPBuildID=111;SSR=0;SAO=0;VP=0x050100080015000102000100;WGT=1;VC=SNV;SLO;INT;OTH;ASP;GNO;CAF=0.04113,0.9105;COMMON=1";
var sa = new SupplementaryAnnotationPosition(141724543);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
foreach (var dbSnpItem in dbsnpReader.ExtractItem(vcfLine1))
{
dbSnpItem.SetSupplementaryAnnotations(saCreator);
}
foreach (var dbSnpItem in dbsnpReader.ExtractItem(vcfLine2))
{
dbSnpItem.SetSupplementaryAnnotations(saCreator);
}
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
saCreator.FinalizePositionalAnnotations();
writer.Write(saCreator, sa.ReferencePosition);
}
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation = reader.GetAnnotation(141724543) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation);
Assert.Equal("C", observedAnnotation.GlobalMajorAllele);
Assert.Equal("0.9105", observedAnnotation.GlobalMajorAlleleFrequency);
Assert.Equal("T", observedAnnotation.GlobalMinorAllele);
Assert.Equal("0.04832", observedAnnotation.GlobalMinorAlleleFrequency);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadWriteCustomAnnotation()
{
var randomPath = GetRandomPath(true);
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var clinVarVersion = new DataSourceVersion("ClinVar", "13.5", DateTime.Parse("2015-01-19").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, clinVarVersion
};
var customFile = new FileInfo(Resources.TopPath("customCosmic.vcf"));
var customReader = new CustomAnnotationReader(customFile, _renamer);
// all items from this file should be of type cosmic.
var customItems = customReader.ToList();
var sa = new SupplementaryAnnotationPosition(69224);
var saCreator = new SupplementaryPositionCreator(sa);
foreach (var customItem in customItems)
{
// NOTE that the two custom items are for different position, but for the purpose of our test, this is not an issue.
customItem.SetSupplementaryAnnotations(saCreator);
}
// the above code was unit tested in MergeDbSnpClinVar()
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(69224);
Assert.NotNull(observedAnnotation1);
for (var i = 0; i < sa.CustomItems.Count; i++)
{
Assert.Equal(sa.CustomItems[i].Id, observedAnnotation1.CustomItems[i].Id);
Assert.Equal(sa.CustomItems[i].AnnotationType, observedAnnotation1.CustomItems[i].AnnotationType);
Assert.Equal(sa.CustomItems[i].IsAlleleSpecific, observedAnnotation1.CustomItems[i].IsAlleleSpecific);
Assert.True(sa.CustomItems[i].StringFields.SequenceEqual(observedAnnotation1.CustomItems[i].StringFields));
if (sa.CustomItems[i].BooleanFields.Count > 0)
{
Assert.True(sa.CustomItems[i].BooleanFields.SequenceEqual(observedAnnotation1.CustomItems[i].BooleanFields));
}
}
}
}
public void ReadWriteClinVar()
{
//test to make sure that we write a ClinVar entry and read back the same thing.
var xmlReader = new ClinVarXmlReader(new FileInfo(@"Resources\RCV000152657.xml"), _reader, _sequence);
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var clinVarVersion = new DataSourceVersion("ClinVar", "13.5", DateTime.Parse("2015-01-19").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, clinVarVersion
};
var sa = new SupplementaryAnnotationPosition(10183457);
var saCreator = new SupplementaryPositionCreator(sa);
foreach (var clinVarItem in xmlReader)
{
clinVarItem.SetSupplementaryAnnotations(saCreator);
saCreator.MergeSaCreator(saCreator);
}
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr9", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
var observedAnnotation = reader.GetAnnotation(10183457) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation);
for (var i = 0; i < sa.ClinVarItems.Count; i++)
{
Assert.Equal(sa.ClinVarItems[i].ID, observedAnnotation.ClinVarItems[i].ID);
Assert.Equal(sa.ClinVarItems[i].Significance, observedAnnotation.ClinVarItems[i].Significance);
Assert.Equal(sa.ClinVarItems[i].LastUpdatedDate, observedAnnotation.ClinVarItems[i].LastUpdatedDate);
Assert.True(sa.ClinVarItems[i].Phenotypes.SequenceEqual(observedAnnotation.ClinVarItems[i].Phenotypes));
Assert.True(sa.ClinVarItems[i].MedGenIDs.SequenceEqual(observedAnnotation.ClinVarItems[i].MedGenIDs));
Assert.True(sa.ClinVarItems[i].OrphanetIDs.SequenceEqual(observedAnnotation.ClinVarItems[i].OrphanetIDs));
Assert.Equal(sa.ClinVarItems[i].AlleleOrigins, observedAnnotation.ClinVarItems[i].AlleleOrigins);
Assert.True(sa.ClinVarItems[i].OmimIDs.SequenceEqual(observedAnnotation.ClinVarItems[i].OmimIDs));
Assert.True(sa.ClinVarItems[i].PubmedIds.SequenceEqual(observedAnnotation.ClinVarItems[i].PubmedIds));
}
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void Utf8ClinVar()
{
// NIR-900
var xmlReader = new ClinVarXmlReader(new FileInfo(Resources.TopPath("RCV000087262.xml")), _reader, _sequence);
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var clinVarVersion = new DataSourceVersion("ClinVar", "13.5", DateTime.Parse("2015-01-19").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, clinVarVersion
};
// This is the case where Nirvana throws an error: Too many bytes in what should have been a 7 bit encoded Int32.
var sa = new SupplementaryAnnotationPosition(225592188);
var saCreator = new SupplementaryPositionCreator(sa);
foreach (var clinVarItem in xmlReader)
{
clinVarItem.SetSupplementaryAnnotations(saCreator);
saCreator.MergeSaCreator(saCreator);
}
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(225592188) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
for (var i = 0; i < sa.ClinVarItems.Count; i++)
{
Assert.Equal(sa.ClinVarItems[i].Phenotypes, observedAnnotation1.ClinVarItems[i].Phenotypes);
}
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public SuppAnnotExtractor(string compressedRefFile, string inputSuppAnnotFile, int begin, int end,
string datasourceName = null, string outDirectory = null)
{
_renamer = ChromosomeRenamer.GetChromosomeRenamer(FileUtilities.GetReadStream(compressedRefFile));
long intervalsPosition;
var saHeader = SupplementaryAnnotationReader.GetHeader(inputSuppAnnotFile, out intervalsPosition);
_begin = begin;
_end = end;
string miniSuppAnnotFile;
if (datasourceName == null)
{
miniSuppAnnotFile = _renamer.GetUcscReferenceName(saHeader.ReferenceSequenceName)
+ '_' + begin.ToString(CultureInfo.InvariantCulture) + '_' +
end.ToString(CultureInfo.InvariantCulture) + ".nsa";
if (outDirectory != null)
{
miniSuppAnnotFile = Path.Combine(outDirectory, miniSuppAnnotFile);
}
}
else
{
miniSuppAnnotFile = _renamer.GetUcscReferenceName(saHeader.ReferenceSequenceName)
+ '_' + begin.ToString(CultureInfo.InvariantCulture) + '_' +
end.ToString(CultureInfo.InvariantCulture) + '_' + datasourceName + ".nsa";
if (outDirectory != null)
{
miniSuppAnnotFile = Path.Combine(outDirectory, miniSuppAnnotFile);
}
}
_writer = new SupplementaryAnnotationWriter(miniSuppAnnotFile, saHeader.ReferenceSequenceName, saHeader.DataSourceVersions);
Console.WriteLine("MiniSA output to: " + miniSuppAnnotFile);
}
public void ReadAndWriteExacWithMultipleAlleles()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var exacVersion = new DataSourceVersion("ExAC", "0.3.1", DateTime.Parse("2016-03-16").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
exacVersion
};
// create our expected supplementary annotations: note AN_adj is modified in this
const string vcfline =
"19 3121452 . TA T,TAA 17262.47 AC_Adj0_Filter AC=6,9;AC_AFR=0,0;AC_AMR=0,0;AC_Adj=0,0;AC_EAS=0,0;AC_FIN=0,0;AC_Het=0,0,0;AC_Hom=0,0;AC_NFE=0,0;AC_OTH=0,0;AC_SAS=0,0;AF=4.587e-03,6.881e-03;AN=1308;AN_AFR=0;AN_AMR=0;AN_Adj=3;AN_EAS=0;AN_FIN=0;AN_NFE=0;AN_OTH=0;AN_SAS=0;BaseQRankSum=0.437;DP=2838";
var sa = new SupplementaryAnnotationPosition(3121453);
var saCreator = new SupplementaryPositionCreator(sa);
var exacReader = new ExacReader(_renamer);
var additionalItems = new List <SupplementaryDataItem>();
foreach (var exacItem in exacReader.ExtractItems(vcfline))
{
var currentItem = exacItem.SetSupplementaryAnnotations(saCreator);
additionalItems.Add(currentItem);
}
var currentSa = new SupplementaryAnnotationPosition(3121453);
var currentSaCreator = new SupplementaryPositionCreator(currentSa);
foreach (var exacItem in additionalItems)
{
exacItem.SetSupplementaryAnnotations(currentSaCreator);
}
// write the supplementary annotation file
using (
var writer = new SupplementaryAnnotationWriter(randomPath, "chr19",
expectedDataSourceVersions))
{
writer.Write(currentSaCreator, currentSa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(3121453) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
// we want to make sure we are reading the values we have written
var expExaciA =
currentSa.AlleleSpecificAnnotations["iA"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(expExaciA);
var obsExaciA =
observedAnnotation1.AlleleSpecificAnnotations["iA"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(obsExaciA);
Assert.Equal(expExaciA.ExacAllAn, obsExaciA.ExacAllAn);
Assert.Equal(expExaciA.ExacCoverage, obsExaciA.ExacCoverage);
Assert.Equal(expExaciA.ExacAllAc, obsExaciA.ExacAllAc);
Assert.NotNull(obsExaciA.ExacAllAc);
Assert.Null(obsExaciA.ExacFinAc);
Assert.Null(obsExaciA.ExacFinAn);
// we want to make sure we are reading the values we have written
var expExac1 =
currentSa.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(expExac1);
var obsExac1 =
observedAnnotation1.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(obsExac1);
Assert.Equal(expExac1.ExacAllAn, obsExac1.ExacAllAn);
Assert.Equal(expExac1.ExacCoverage, obsExac1.ExacCoverage);
Assert.Equal(expExac1.ExacAllAc, obsExac1.ExacAllAc);
Assert.NotNull(obsExac1.ExacAllAc);
Assert.Null(obsExac1.ExacFinAc);
Assert.Null(obsExac1.ExacFinAn);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadWriteWithSuppIntervals()
{
// NIR-1359
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion
};
// This is the case where Nirvana throws an error: Too many bytes in what should have been a 7 bit encoded Int32.
var sa = new SupplementaryAnnotationPosition(5073770);
var saCreator = new SupplementaryPositionCreator(sa);
// adding a supplementary interval
var intValues = new Dictionary <string, int>();
var doubleValues = new Dictionary <string, double>();
var freqValues = new Dictionary <string, double>();
var stringValues = new Dictionary <string, string>();
var boolValues = new List <string>();
var suppInterval = new SupplementaryInterval(5073770, 5073970, "chr1", "<DUP>", VariantType.duplication, "ClinVar", _renamer, intValues,
doubleValues, freqValues, stringValues, boolValues);
suppInterval.AddStringValue("ID", "RandomClin001");
// the above code was unit tested in MergeDbSnpClinVar()
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr9", expectedDataSourceVersions))
{
writer.SetIntervalList(new List <SupplementaryInterval> {
suppInterval
});
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// read the stored intervals
var suppIntervals = reader.GetSupplementaryIntervals(_renamer).ToList();
Assert.Equal(1, suppIntervals.Count);
foreach (var interval in suppIntervals)
{
Assert.Equal(5073770, interval.Start);
Assert.Equal(5073970, interval.End);
Assert.Equal("<DUP>", interval.AlternateAllele);
Assert.Equal("ClinVar", interval.Source);
Assert.Equal("duplication", interval.VariantType.ToString());
foreach (var keyValuePair in interval.StringValues)
{
if (keyValuePair.Key == "ID")
{
Assert.Equal("RandomClin001", keyValuePair.Value);
}
if (keyValuePair.Key == "vid")
{
Assert.Equal("1:5073770:5073970", keyValuePair.Value);
}
}
}
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadWriteDbSnpCosmic()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var cosmicVersion = new DataSourceVersion("COSMIC", "GRCh37_v71", DateTime.Parse("2014-10-21").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, cosmicVersion
};
// create our expected supplementary annotations
const string vcfLine1 = "1 10228 rs143255646 TA T . . RS=143255646;RSPOS=10229;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
var sa = new SupplementaryAnnotationPosition(10229);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem1.SetSupplementaryAnnotations(saCreator)
};
var cosmicItem1 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, null);
var cosmicItem2 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, null);
additionalItems.Add(cosmicItem1.SetSupplementaryAnnotations(saCreator));
additionalItems.Add(cosmicItem2.SetSupplementaryAnnotations(saCreator));
//sa.Clear();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(saCreator);
}
Assert.Equal(1, sa.CosmicItems.Count);
// the preceeding code has been unit tested in MergeDbSnpCosmic()
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(10229) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnp =
sa.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(expDbSnp);
var obsDbSnp =
observedAnnotation1.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(obsDbSnp);
Assert.Equal(expDbSnp.DbSnp, obsDbSnp.DbSnp);
Assert.True(observedAnnotation1.ContainsCosmicId(sa.CosmicItems[0].ID));
Assert.Equal(1, observedAnnotation1.CosmicItems.Count);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadWriteExacDbsnp()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var cosmicVersion = new DataSourceVersion("COSMIC", "GRCh37_v71", DateTime.Parse("2014-10-21").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, cosmicVersion
};
// create our expected supplementary annotations
const string vcfLine1 = "2 48010488 rs1042821 G A . . RS=1042821;RSPOS=48010488;RV;dbSNPBuildID=86;SSR=0;SAO=1;VP=0x050168420a05150136100100;GENEINFO=MSH6:2956;WGT=1;VC=SNV;PM;PMC;SLO;NSM;REF;U5;R5;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;LSD;CAF=0.7991,0.2009;COMMON=1";
const string vcfLine2 =
"2 48010488 rs1042821 G A,C 14068898.15 PASS AC=21019,1;AC_AFR=1700,0;AC_AMR=1015,1;AC_Adj=19510,1;AC_EAS=1973,0;AC_FIN=743,0;AC_Het=15722,1,0;AC_Hom=1894,0;AC_NFE=10593,0;AC_OTH=147,0;AC_SAS=3339,0;AF=0.178,8.487e-06;AN=117830;AN_AFR=6388;AN_AMR=9014;AN_Adj=91130;AN_EAS=6792;AN_FIN=5078;AN_NFE=48404;AN_OTH=664;AN_SAS=14790;BaseQRankSum=-4.850e-01;ClippingRankSum=-1.400e-01;DB;DP=1206681;FS=0.000;GQ_MEAN=129.86;GQ_STDDEV=221.88;Het_AFR=1322,0,0;Het_AMR=931,1,0;Het_EAS=1511,0,0;Het_FIN=665,0,0;Het_NFE=8585,0,0;Het_OTH=111,0,0;Het_SAS=2597,0,0;Hom_AFR=189,0;Hom_AMR=42,0;Hom_EAS=231,0;Hom_FIN=39,0;Hom_NFE=1004,0;Hom_OTH=18,0;Hom_SAS=371,0;InbreedingCoeff=0.0376;MQ=60.00;MQ0=0;MQRankSum=0.00;NCC=3737;POSITIVE_TRAIN_SITE;QD=17.46;ReadPosRankSum=0.181;VQSLOD=5.87;culprit=MQ;DP_HIST=3051|9435|11318|5521|9711|11342|4131|1270|615|404|328|266|264|262|196|186|126|115|97|277,133|968|2180|3402|3564|2815|1772|954|551|389|321|263|261|261|196|186|126|115|97|277,0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=949|2966|347|492|15135|1435|1335|854|421|526|590|416|13672|1951|445|462|255|174|211|16279,24|79|81|124|135|96|110|118|97|180|228|137|182|191|126|171|180|151|192|16229,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1";
var sa = new SupplementaryAnnotationPosition(48010488);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
dbSnpItem1.SetSupplementaryAnnotations(saCreator);
var exacReader = new ExacReader(_renamer);
foreach (var exacItem in exacReader.ExtractItems(vcfLine2))
{
exacItem.SetSupplementaryAnnotations(saCreator);
}
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr2", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(48010488) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnpA =
sa.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
var obsDbSnpA =
observedAnnotation1.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
Assert.NotNull(expDbSnpA);
Assert.NotNull(obsDbSnpA);
// we want to make sure we are reading the values we have written
Assert.Equal(expDbSnpA.DbSnp, obsDbSnpA.DbSnp);
var expExacA =
sa.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
var obsExacA =
observedAnnotation1.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
Assert.NotNull(expExacA);
Assert.NotNull(obsExacA);
Assert.Equal(expExacA.ExacAllAn, obsExacA.ExacAllAn);
Assert.Equal(expExacA.ExacCoverage, obsExacA.ExacCoverage);
Assert.Equal(Convert.ToDouble(expExacA.ExacAllAc), Convert.ToDouble(obsExacA.ExacAllAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacAfrAc), Convert.ToDouble(obsExacA.ExacAfrAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacAmrAc), Convert.ToDouble(obsExacA.ExacAmrAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacEasAc), Convert.ToDouble(obsExacA.ExacEasAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacFinAc), Convert.ToDouble(obsExacA.ExacFinAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacNfeAc), Convert.ToDouble(obsExacA.ExacNfeAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacOthAc), Convert.ToDouble(obsExacA.ExacOthAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacSasAc), Convert.ToDouble(obsExacA.ExacSasAc));
var expExacC =
sa.AlleleSpecificAnnotations["C"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
var obsExacC =
observedAnnotation1.AlleleSpecificAnnotations["C"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
Assert.NotNull(expExacC);
Assert.NotNull(obsExacC);
Assert.Equal(expExacC.ExacCoverage, obsExacC.ExacCoverage);
Assert.Equal(Convert.ToDouble(expExacC.ExacAllAc), Convert.ToDouble(obsExacC.ExacAllAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacAfrAc), Convert.ToDouble(obsExacC.ExacAfrAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacAmrAc), Convert.ToDouble(obsExacC.ExacAmrAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacEasAc), Convert.ToDouble(obsExacC.ExacEasAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacFinAc), Convert.ToDouble(obsExacC.ExacFinAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacNfeAc), Convert.ToDouble(obsExacC.ExacNfeAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacOthAc), Convert.ToDouble(obsExacC.ExacOthAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacSasAc), Convert.ToDouble(obsExacC.ExacSasAc));
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void MultiAlleleMergeDbSnp1KpEvsSaRw()
{
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var oneKGenVersion = new DataSourceVersion("1000 Genomes Project", "phase3_shapeit2_mvncall_integrated_v5.", DateTime.Parse("2013-05-02").Ticks);
var evsDataSource = new DataSourceVersion("EVS", "V2", DateTime.Parse("2013-11-13").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, oneKGenVersion, evsDataSource
};
// create our expected supplementary annotations
const string vcfLine1 = "1 1564952 rs112177324 TG T . . RS=112177324;RSPOS=1564953;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x05010008000514013e000200;WGT=1;VC=DIV;SLO;INT;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.8468,0.1506;COMMON=1";
const string vcfLine2 = "1 1564952 rs112177324 TG TGG,T 100 PASS AC=13,754;AF=0.00259585,0.150559;AN=5008;NS=2504;DP=8657;EAS_AF=0,0.0933;AMR_AF=0.0014,0.2046;AFR_AF=0.0091,0.0182;EUR_AF=0,0.3588;SAS_AF=0,0.136";
const string vcfLine3 = "1 1564952 rs112177324 TG TGG,T . PASS BSNP=dbSNP_132;EA_AC=2,3039,4701;AA_AC=44,279,3231;TAC=46,3318,7932;MAF=39.2793,9.0884,29.7805;GTS=A1A1,A1A2,A1R,A2A2,A2R,RR;EA_GTC=0,1,1,707,1624,1538;AA_GTC=4,4,32,41,193,1503;GTC=4,5,33,748,1817,3041;DP=10;GL=MIB2;CP=0.8;CG=-0.0;AA=.;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_080875.2:intron,NM_080875.2:intron,NM_001170689.1:intron,NM_001170689.1:intron,NM_001170688.1:intron,NM_001170688.1:intron,NM_001170687.1:intron,NM_001170687.1:intron,NM_001170686.1:intron,NM_001170686.1:intron;HGVS_CDNA_VAR=NM_080875.2:c.2908+7del1,NM_080875.2:c.2908+6_2908+7insG,NM_001170689.1:c.2187-66del1,NM_001170689.1:c.2187-67_2187-66insG,NM_001170688.1:c.2713+7del1,NM_001170688.1:c.2713+6_2713+7insG,NM_001170687.1:c.2866+7del1,NM_001170687.1:c.2866+6_2866+7insG,NM_001170686.1:c.2896+7del1,NM_001170686.1:c.2896+6_28967insG;HGVS_PROTEIN_VAR=.,.,.,.,.,.,.,.,.,.;CDS_SIZES=NM_080875.2:3213,NM_080875.2:3213,NM_001170689.1:2262,NM_001170689.1:2262,NM_001170688.1:3018,NM_001170688.1:3018,NM_001170687.1:3171,NM_001170687.1:3171,NM_001170686.1:3201,NM_001170686.1:3201;GS=.,.,.,.,.,.,.,.,.,.;PH=.,.,.,.,.,.,.,.,.,.;EA_AGE=.;AA_AGE=.";
var sa = new SupplementaryAnnotationPosition(1564953);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem.SetSupplementaryAnnotations(saCreator)
};
var oneKGenReader = new OneKGenReader(_renamer);
var oneKGenItem = oneKGenReader.ExtractItems(vcfLine2)[0];
additionalItems.Add(oneKGenItem.SetSupplementaryAnnotations(saCreator));
var evsReader = new EvsReader(_renamer);
var evsItemsList = evsReader.ExtractItems(vcfLine3);
foreach (var evsItem in evsItemsList)
{
additionalItems.Add(evsItem.SetSupplementaryAnnotations(saCreator));
}
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(saCreator);
}
// write the supplementary annotation file
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
var observedDataSourceVersions = reader.Header.DataSourceVersions;
// check the data source versions
Assert.Equal(observedDataSourceVersions.Count, 3);
var observedDataSourceVersion = observedDataSourceVersions[0];
Assert.Equal(dbSnpVersion.Name, observedDataSourceVersion.Name);
Assert.Equal(dbSnpVersion.Version, observedDataSourceVersion.Version);
Assert.Equal(dbSnpVersion.ReleaseDateTicks, observedDataSourceVersion.ReleaseDateTicks);
// checking the global alleles
Assert.Null(sa.GlobalMajorAllele);
Assert.Null(sa.GlobalMajorAlleleFrequency);
Assert.Null(sa.GlobalMinorAllele);
Assert.Null(sa.GlobalMinorAlleleFrequency);
// extract the three annotations
var observedAnnotation = reader.GetAnnotation(1564953) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation);
var expectedInsOneKgAllAc = ((OneKGenAnnotation)sa.AlleleSpecificAnnotations["iG"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]).OneKgAllAc;
var expectedDelHasOneKg = sa.AlleleSpecificAnnotations["1"].HasDataSource(DataSourceCommon.DataSource.OneKg);
var expectedInsEvsAfr = ((EvsAnnotation)sa.AlleleSpecificAnnotations["iG"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)]).EvsAfr;
var expectedInsHasDbSnp = sa.AlleleSpecificAnnotations["iG"].HasDataSource(DataSourceCommon.DataSource.DbSnp);
var obsAsaIns = observedAnnotation.AlleleSpecificAnnotations["iG"];
var obsAsaDel = observedAnnotation.AlleleSpecificAnnotations["1"];
Assert.Equal(expectedInsOneKgAllAc, ((OneKGenAnnotation)obsAsaIns.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]).OneKgAllAc);
Assert.Equal(expectedDelHasOneKg, obsAsaDel.HasDataSource(DataSourceCommon.DataSource.OneKg));
Assert.Equal(expectedInsEvsAfr, ((EvsAnnotation)obsAsaIns.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)]).EvsAfr);
Assert.Equal(expectedInsHasDbSnp, obsAsaIns.HasDataSource(DataSourceCommon.DataSource.DbSnp));
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadAndWriteDbSnp1KgEvs()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var oneKGenVersion = new DataSourceVersion("1000 Genomes Project", "phase3_shapeit2_mvncall_integrated_v5.", DateTime.Parse("2013-05-02").Ticks);
var evsDataSource = new DataSourceVersion("EVS", "V2", DateTime.Parse("2013-11-13").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, oneKGenVersion, evsDataSource
};
// create our expected supplementary annotations
const string vcfLine1 = "1 69428 rs140739101 T G . . RS=140739101;RSPOS=69428;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050200000a05140026000100;WGT=1;VC=SNV;S3D;NSM;REF;ASP;VLD;KGPhase3;CAF=0.981,0.01897;COMMON=1";
const string vcfLine2 = "1 69428 rs140739101 T G 100 PASS AC=95;AF=0.0189696;AN=5008;NS=2504;DP=17611;EAS_AF=0.003;AMR_AF=0.036;AFR_AF=0.0015;EUR_AF=0.0497;SAS_AF=0.0153;AA=.|||";
const string vcfLine3 = "1 69428 rs140739101 T G . PASS BSNP=dbSNP_134;EA_AC=313,6535;AA_AC=14,3808;TAC=327,10343;MAF=4.5707,0.3663,3.0647;GTS=GG,GT,TT;EA_GTC=92,129,3203;AA_GTC=1,12,1898;GTC=93,141,5101;DP=110;GL=OR4F5;CP=1.0;CG=0.9;AA=T;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_001005484.1:missense;HGVS_CDNA_VAR=NM_001005484.1:c.338T>G;HGVS_PROTEIN_VAR=NM_001005484.1:p.(F113C);CDS_SIZES=NM_001005484.1:918;GS=205;PH=probably-damaging:0.999;EA_AGE=.;AA_AGE=.";
const string altAllele = "G";
var sa = new SupplementaryAnnotationPosition(69428);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem = dbsnpReader.ExtractItem(vcfLine1)[0];
dbSnpItem.SetSupplementaryAnnotations(saCreator);
var oneKGenReader = new OneKGenReader(_renamer);
var oneKGenItem = oneKGenReader.ExtractItems(vcfLine2)[0];
oneKGenItem.SetSupplementaryAnnotations(saCreator);
var evsReader = new EvsReader(_renamer);
var evsItem = evsReader.ExtractItems(vcfLine3)[0];
evsItem.SetSupplementaryAnnotations(saCreator);
// the preceeding code has been unit tested in MergeDbSnp1kpEvs()
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
var observedDataSourceVersions = reader.Header.DataSourceVersions;
// check the data source versions
Assert.Equal(observedDataSourceVersions.Count, 3);
var observedDataSourceVersion = observedDataSourceVersions[0];
Assert.Equal(dbSnpVersion.Name, observedDataSourceVersion.Name);
Assert.Equal(dbSnpVersion.Version, observedDataSourceVersion.Version);
Assert.Equal(dbSnpVersion.ReleaseDateTicks, observedDataSourceVersion.ReleaseDateTicks);
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(69428) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnp =
sa.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]
as DbSnpAnnotation;
Assert.NotNull(expDbSnp);
var expOneKg =
sa.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]
as OneKGenAnnotation;
Assert.NotNull(expOneKg);
var expEvs =
sa.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)]
as EvsAnnotation;
Assert.NotNull(expEvs);
var obsDbSnp = observedAnnotation1.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]
as DbSnpAnnotation;
Assert.NotNull(obsDbSnp);
var obsOneKg = observedAnnotation1.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]
as OneKGenAnnotation;
Assert.NotNull(obsOneKg);
var obsEvs = observedAnnotation1.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)]
as EvsAnnotation;
Assert.NotNull(obsEvs);
Assert.Equal(expDbSnp.DbSnp, obsDbSnp.DbSnp);
Assert.Equal(expEvs.EvsAll, obsEvs.EvsAll);
Assert.Equal(expOneKg.OneKgAllAc, obsOneKg.OneKgAllAc);
Assert.Equal(expEvs.EvsCoverage, obsEvs.EvsCoverage);
Assert.Equal(expEvs.NumEvsSamples, obsEvs.NumEvsSamples);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadAndWrite()
{
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(_randomPath))
{
var observedDataSourceVersions = reader.Header.DataSourceVersions;
var refSeq = reader.Header.ReferenceSequenceName;
var dataVersion = reader.Header.DataVersion;
var creationTime = reader.Header.CreationTimeTicks;
var genomeAssembly = reader.Header.GenomeAssembly;
// check the data source versions
Assert.Equal(observedDataSourceVersions.Count, 1);
var observedDataSourceVersion = observedDataSourceVersions[0];
Assert.Equal(_expectedDataSourceVersion.Name, observedDataSourceVersion.Name);
Assert.Equal(_expectedDataSourceVersion.Version, observedDataSourceVersion.Version);
Assert.Equal(_expectedDataSourceVersion.ReleaseDateTicks, observedDataSourceVersion.ReleaseDateTicks);
Assert.NotNull(refSeq);
Assert.Equal(SupplementaryAnnotationCommon.DataVersion, dataVersion);
Assert.True(DateTime.MinValue.Ticks != creationTime);
Assert.True(genomeAssembly == GenomeAssembly.Unknown);
var expDbsnp1 =
((DbSnpAnnotation)
_expectedAnnotation1.AlleleSpecificAnnotations[AltAllele].Annotations[
DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]).DbSnp;
var expDbsnp2 =
((DbSnpAnnotation)
_expectedAnnotation2.AlleleSpecificAnnotations[AltAllele].Annotations[
DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]).DbSnp;
var expDbsnp3 =
((DbSnpAnnotation)
_expectedAnnotation3.AlleleSpecificAnnotations[AltAllele].Annotations[
DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]).DbSnp;
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(100) as SupplementaryAnnotationPosition;
var observedAnnotation2 = reader.GetAnnotation(101) as SupplementaryAnnotationPosition;
var observedAnnotation3 = reader.GetAnnotation(102) as SupplementaryAnnotationPosition;
var obsDbsnp1 =
((DbSnpAnnotation)
observedAnnotation1.AlleleSpecificAnnotations[AltAllele].Annotations[
DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]).DbSnp;
var obsDbsnp2 =
((DbSnpAnnotation)
observedAnnotation2.AlleleSpecificAnnotations[AltAllele].Annotations[
DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]).DbSnp;
var obsDbsnp3 =
((DbSnpAnnotation)
observedAnnotation3.AlleleSpecificAnnotations[AltAllele].Annotations[
DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]).DbSnp;
Assert.Equal(expDbsnp1, obsDbsnp1);
Assert.Equal(expDbsnp2, obsDbsnp2);
Assert.Equal(expDbsnp3, obsDbsnp3);
// jump around the file
var observedJumpAnnotation2 = reader.GetAnnotation(_expectedAnnotation2.ReferencePosition) as SupplementaryAnnotationPosition;
var observedJumpAnnotation1 = reader.GetAnnotation(_expectedAnnotation1.ReferencePosition) as SupplementaryAnnotationPosition;
var observedJumpAnnotation3 = reader.GetAnnotation(_expectedAnnotation3.ReferencePosition) as SupplementaryAnnotationPosition;
var obsJumpDbsnp1 =
((DbSnpAnnotation)
observedJumpAnnotation1.AlleleSpecificAnnotations[AltAllele].Annotations[
DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]).DbSnp;
var obsJumpDbsnp2 =
((DbSnpAnnotation)
observedJumpAnnotation2.AlleleSpecificAnnotations[AltAllele].Annotations[
DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]).DbSnp;
var obsJumpDbsnp3 =
((DbSnpAnnotation)
observedJumpAnnotation3.AlleleSpecificAnnotations[AltAllele].Annotations[
DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]).DbSnp;
Assert.Equal(expDbsnp1, obsJumpDbsnp1);
Assert.Equal(expDbsnp2, obsJumpDbsnp2);
Assert.Equal(expDbsnp3, obsJumpDbsnp3);
var observedInterval = reader.GetSupplementaryIntervals(_renamer);
Assert.Equal(_expectedInterval, observedInterval.First());
}
}
