private void CreateCustIntervalTsv(string fileName)
{
if (string.IsNullOrEmpty(fileName))
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(fileName);
var reader = new CustomIntervalParser(new FileInfo(fileName), _refNamesDictionary);
using (var writer = new IntervalTsvWriter(_outputDirectory, version,
_genomeAssembly.ToString(), SaTsvCommon.CustIntervalSchemaVersion, reader.KeyName,
ReportFor.AllVariants))
{
foreach (var custInterval in reader.GetCustomIntervals())
{
writer.AddEntry(custInterval.Chromosome.EnsemblName, custInterval.Start, custInterval.End, custInterval.GetJsonString());
}
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("customInterval", fileName, timeSpan);
}
public void CustomIntervalTypeReaderTest()
{
var customFile = new FileInfo(Resources.TopPath("icslInterval.bed"));
var customReader = new CustomIntervalParser(customFile, _refChromDict);
// all items from this file should be of type cosmic.
foreach (var customInterval in customReader.GetCustomIntervals())
{
Assert.Equal("IcslIntervals", customInterval.Type);
}
}
public CustomIntervalDbCreator(string bedFile, string outputDirectory, ChromosomeRenamer renamer)
{
if (bedFile == null)
{
return;
}
_renamer = renamer;
_outputDirectory = outputDirectory;
_observedRefSeq = new HashSet <string>();
_intervalParser = new CustomIntervalParser(new FileInfo(bedFile), renamer);
_dataVersion = AddSourceVersion(bedFile);
}
public void InforFieldsTest()
{
var customFile = new FileInfo(Resources.TopPath("icslInterval.bed"));
var customReader = new CustomIntervalParser(customFile, _refChromDict);
// all items from this file should be of type cosmic.
var i = 0;
foreach (var customInterval in customReader.GetCustomIntervals())
{
switch (i)
{
case 0: //checking the first item
Assert.Equal("chr1", customInterval.Chromosome.UcscName);
Assert.Equal(69091, customInterval.Start);
Assert.Equal(70008, customInterval.End);
Assert.Equal("OR4F5", customInterval.StringValues["gene"]);
Assert.Equal("0.0", customInterval.NonStringValues["score"]);
Assert.Equal("3.60208899915", customInterval.NonStringValues["exacScore"]);
Assert.Equal("Some_evidence_of_constraint", customInterval.StringValues["assesment"]);
break;
case 1:
Assert.Equal("chr1", customInterval.Chromosome.UcscName);
Assert.Equal(861121, customInterval.Start);
Assert.Equal(879582, customInterval.End);
Assert.Equal("SAMD11", customInterval.StringValues["gene"]);
Assert.Equal("0.997960686608", customInterval.NonStringValues["score"]);
Assert.Equal("-3.7861959419", customInterval.NonStringValues["exacScore"]);
Assert.Equal("Minimal_evidence_of_constraint", customInterval.StringValues["assesment"]);
break;
}
i++;
}
}