private static void WriteGeneralAttributes(StreamWriter writer, RegulatoryElement regulatoryFeature)
{
if (!regulatoryFeature.Id.IsEmpty)
{
writer.Write($"regulatory_feature_id \"{regulatoryFeature.Id}\"; ");
}
writer.Write($"regulatory_feature_type \"{regulatoryFeature.Type}\"; ");
}
public void RegulatoryFeatureEqualityTests()
{
var regulatoryFeature1 = new RegulatoryElement(2, 100, 200, CompactId.Convert("1"), RegulatoryElementType.promoter);
var regulatoryFeature2 = new RegulatoryElement(2, 100, 200, CompactId.Convert("1"), RegulatoryElementType.promoter);
var regulatoryFeature3 = new RegulatoryElement(4, 105, 201, CompactId.Convert("3"), RegulatoryElementType.CTCF_binding_site);
Assert.Equal(regulatoryFeature1, regulatoryFeature2);
Assert.False(regulatoryFeature1 == regulatoryFeature3);
}
public void AddRegulatoryFeature(RegulatoryElement regulatoryFeature, VariantAlternateAllele altAllele, string[] consequences)
{
var regulatoryRegion = new JsonVariant.RegulatoryRegion
{
ID = regulatoryFeature.Id.ToString(),
Type = regulatoryFeature.Type.ToString(),
Consequence = consequences
};
FindCorrespondingJsonVariant(altAllele);
_currJsonVariant.RegulatoryRegions.Add(regulatoryRegion);
}
public void ReadWriteTests()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
var regulatoryFeature1 = new RegulatoryElement(2, 100, 200, CompactId.Convert("1"), RegulatoryElementType.promoter);
var regulatoryFeature2 = new RegulatoryElement(3, 100, 200, CompactId.Convert("2"), RegulatoryElementType.enhancer);
var regulatoryFeature3 = new RegulatoryElement(4, 105, 201, CompactId.Convert("3"), RegulatoryElementType.CTCF_binding_site);
using (var writer = new ExtendedBinaryWriter(FileUtilities.GetCreateStream(randomPath)))
{
regulatoryFeature1.Write(writer);
regulatoryFeature2.Write(writer);
regulatoryFeature3.Write(writer);
}
using (var reader = new ExtendedBinaryReader(FileUtilities.GetReadStream(randomPath)))
{
Assert.Equal(regulatoryFeature1, RegulatoryElement.Read(reader));
Assert.Equal(regulatoryFeature2, RegulatoryElement.Read(reader));
Assert.Equal(regulatoryFeature3, RegulatoryElement.Read(reader));
}
File.Delete(randomPath);
}
public void RegulatoryFeatureToStringTests()
{
var regulatoryFeature1 = new RegulatoryElement(2, 100, 200, CompactId.Convert("1"), RegulatoryElementType.promoter);
Assert.NotNull(regulatoryFeature1.ToString());
}
private static void WriteRegulatoryFeature(StreamWriter writer, string[] referenceNames, RegulatoryElement regulatoryFeature)
{
writer.Write($"{referenceNames[regulatoryFeature.ReferenceIndex]}\t.\tregulatory feature\t{regulatoryFeature.Start}\t{regulatoryFeature.End}\t.\t.\t.\t");
WriteGeneralAttributes(writer, regulatoryFeature);
writer.WriteLine();
}