private void CreateDbsnpGaTsv(string fileName)
{
if (fileName == null)
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(fileName);
var dbsnpWriter = new SaTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(),
SaTsvCommon.DbSnpSchemaVersion, InterimSaCommon.DbsnpTag, null, true, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)));
var globalAlleleWriter = new SaTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(),
SaTsvCommon.DbSnpSchemaVersion, InterimSaCommon.GlobalAlleleTag, "GMAF", false, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)));
using (var tsvWriter = new DbsnpGaTsvWriter(dbsnpWriter, globalAlleleWriter))
{
var dbSnpReader = new DbSnpReader(GZipUtilities.GetAppropriateReadStream(fileName), _refNamesDictionary);
TsvWriterUtilities.WriteSortedItems(dbSnpReader.GetDbSnpItems(), tsvWriter);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("DbSNP", version.Version, timeSpan);
}
public void same_Frequency_alts_return_the_first_one()
{
var alleleFreqDict = new Dictionary <string, double>
{
{ "A", 0.2 },
{ "G", 0.4 },
{ "T", 0.4 }
};
var mostFrequent = DbsnpGaTsvWriter.GetMostFrequentAllele(alleleFreqDict, "A");
Assert.Equal("G", mostFrequent);
}
public void Same_Frequency_ref_and_alt_and_ref_is_not_preferred_return_alt_as_gloabal_major()
{
var alleleFreqDict = new Dictionary <string, double>
{
{ "A", 0.4 },
{ "G", 0.4 },
{ "C", 0.2 }
};
var mostFrequent = DbsnpGaTsvWriter.GetMostFrequentAllele(alleleFreqDict, "A", false);
Assert.Equal("G", mostFrequent);
}
private void DbsnpGaTsvWriter_write_sa_item()
{
var chromosome = new Chromosome("chr1", "1", 0);
var chromDict = new Dictionary <string, IChromosome>
{
{ "chr1", chromosome },
{ "1", chromosome }
};
var randomDbsnpPath = Path.GetTempPath();
var sequenceProvider = new Mock <ISequenceProvider>();
var simpleSequence = new SimpleSequence("ATGCGGT", 99);
sequenceProvider.SetupGet(x => x.Sequence).Returns(simpleSequence);
sequenceProvider.Setup(x => x.RefNameToChromosome).Returns(chromDict);
var dataVersion = new DataSourceVersion("dbsnp", "77", 123456);
var dbsnpWriter = new SaTsvWriter(randomDbsnpPath, dataVersion, "GRCh37", 10, "dbsnp", "dbsnp", true, sequenceProvider.Object);
var globalAlleleWriter = new SaTsvWriter(randomDbsnpPath, dataVersion, "GRCh37", 10, "globalAllele", "GMAF", true, sequenceProvider.Object);
using (var dbsnpGaTsvWriter = new DbsnpGaTsvWriter(dbsnpWriter, globalAlleleWriter))
{
var dbSnpItemsPos100 = new List <SupplementaryDataItem>
{
new DbSnpItem(chromosome, 100, 123456, "A", 0.2, "G", 0.4),
new DbSnpItem(chromosome, 100, 123458, "A", 0.2, "T", 0.4)
};
var dbSnpItemsPos103 = new List <SupplementaryDataItem>
{
new DbSnpItem(chromosome, 103, 134567, "C", 0.5, "A", 0.5)
};
var dbSnpItemsPos104 = new List <SupplementaryDataItem>
{
new DbSnpItem(chromosome, 104, 134590, "G", double.MinValue, "A", 0.75)
};
var dbSnpItemsPos106 = new List <SupplementaryDataItem>
{
new DbSnpItem(chromosome, 106, 134257, "T", 0.3, "G", 0.45),
new DbSnpItem(chromosome, 106, 126753, "T", 0.3, "A", 0.25)
};
dbsnpGaTsvWriter.WritePosition(dbSnpItemsPos100);
dbsnpGaTsvWriter.WritePosition(dbSnpItemsPos103);
dbsnpGaTsvWriter.WritePosition(dbSnpItemsPos104);
dbsnpGaTsvWriter.WritePosition(dbSnpItemsPos106);
}
var dbsnpFile = Path.Combine(randomDbsnpPath, "dbsnp_77.tsv.gz");
var globalAlleleFile = Path.Combine(randomDbsnpPath, "globalAllele_77.tsv.gz");
var tsvReader = new ParallelSaTsvReader(dbsnpFile);
using (var tsvEnumerator = tsvReader.GetItems("1").GetEnumerator())
{
Assert.True(tsvEnumerator.MoveNext());
Assert.Equal("\"ids\":[\"rs123456\"]", tsvEnumerator.Current.JsonStrings[0]);
Assert.True(tsvEnumerator.MoveNext());
Assert.Equal("\"ids\":[\"rs123458\"]", tsvEnumerator.Current.JsonStrings[0]);
}
var globalAlleleReader = new ParallelSaTsvReader(globalAlleleFile);
var globalAlleleEnumerator = globalAlleleReader.GetItems("1").GetEnumerator();
Assert.True(globalAlleleEnumerator.MoveNext());
Assert.Equal(100, globalAlleleEnumerator.Current.Position);
Assert.Equal("\"globalMinorAllele\":\"T\",\"globalMinorAlleleFrequency\":0.4", globalAlleleEnumerator.Current.JsonStrings[0]);
Assert.True(globalAlleleEnumerator.MoveNext());
Assert.Equal(103, globalAlleleEnumerator.Current.Position);
Assert.Equal("\"globalMinorAllele\":\"A\",\"globalMinorAlleleFrequency\":0.5", globalAlleleEnumerator.Current.JsonStrings[0]);
Assert.True(globalAlleleEnumerator.MoveNext());
Assert.Equal(104, globalAlleleEnumerator.Current.Position);
Assert.Equal("", globalAlleleEnumerator.Current.JsonStrings[0]);
Assert.True(globalAlleleEnumerator.MoveNext());
Assert.Equal(106, globalAlleleEnumerator.Current.Position);
Assert.Equal("\"globalMinorAllele\":\"T\",\"globalMinorAlleleFrequency\":0.3", globalAlleleEnumerator.Current.JsonStrings[0]);
globalAlleleEnumerator.Dispose();
File.Delete(dbsnpFile);
File.Delete(globalAlleleFile);
}
