public void IsProximal()
{
var variantSite1 = new VariantSite(123);
var variantSite2 = new VariantSite(126);
// Must be less than phasing distance
Assert.True(NeighborhoodBuilder.IsProximal(variantSite1, variantSite2, 4));
Assert.False(NeighborhoodBuilder.IsProximal(variantSite1, variantSite2, 3));
// Works both ways
Assert.True(NeighborhoodBuilder.IsProximal(variantSite1, variantSite2, 4));
Assert.False(NeighborhoodBuilder.IsProximal(variantSite1, variantSite2, 3));
}
protected override void Context()
{
base.Context();
var drugMoleculeBuilder = createMoleculeBuilder("Drug");
var localParameterWithCondition = DomainHelperForSpecs.ConstantParameterWithValue(3)
.WithName("LocalParameterWithCondition")
.WithMode(ParameterBuildMode.Local)
.WithParentContainer(drugMoleculeBuilder);
localParameterWithCondition.ContainerCriteria = Create.Criteria(x => x.With("Cell"));
_molecules = new MoleculeBuildingBlock
{
drugMoleculeBuilder,
createMoleculeBuilder("Other")
};
_spatialStructure = new SpatialStructure
{
NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS),
GlobalMoleculeDependentProperties = new Container()
};
_globalParameter = new Parameter().WithName("GlobalMoleculeParameter").WithFormula(new ConstantFormula(2));
_spatialStructure.GlobalMoleculeDependentProperties.Add(_globalParameter);
var topContainer = new Container().WithName("Organism");
var organ = new Container().WithName("Organ").WithParentContainer(topContainer);
var cell = new Container().WithName("Cell").WithParentContainer(organ).WithMode(ContainerMode.Physical);
var interstitial = new Container().WithName("Interstitial").WithParentContainer(organ).WithMode(ContainerMode.Physical);
var mp = new Container().WithName(Constants.MOLECULE_PROPERTIES).WithParentContainer(organ);
new Parameter().WithName("Local").WithFormula(new ConstantFormula(3)).WithParentContainer(mp);
_spatialStructure.AddTopContainer(topContainer);
var neighborhood = new NeighborhoodBuilder().WithName("A2B");
var nmp = new Container().WithName(Constants.MOLECULE_PROPERTIES).WithParentContainer(neighborhood);
new Parameter().WithName("Hallo").WithFormula(new ConstantFormula(4)).WithParentContainer(nmp);
_spatialStructure.AddNeighborhood(neighborhood);
}
protected override void Context()
{
base.Context();
var n1 = new NeighborhoodBuilder().WithName("cell2int");
var n2 = new NeighborhoodBuilder().WithName("cell2int");
var tc1 = new Container().WithName("Root");
var cell1 = new Container().WithName("Cell").WithParentContainer(tc1);
var int1 = new Container().WithName("int").WithParentContainer(tc1);
n1.FirstNeighbor = cell1;
n1.SecondNeighbor = int1;
var tc2 = new Container().WithName("Root");
var cell2 = new Container().WithName("Cell").WithParentContainer(tc2);
var int2 = new Container().WithName("int").WithParentContainer(tc2);
n2.FirstNeighbor = cell2;
n2.SecondNeighbor = int2;
_object1 = n1;
_object2 = n2;
}
protected override void Context()
{
base.Context();
_molecules = new MoleculeBuildingBlock();
_molecules.Add(createMoleculeBuilder("Drug"));
_molecules.Add(createMoleculeBuilder("Other"));
_spatialStrcuture = new SpatialStructure();
_spatialStrcuture.NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS);
_spatialStrcuture.GlobalMoleculeDependentProperties = new Container();
_globalParameter = new Parameter().WithName("GlobalMoleculeParameter").WithFormula(new ConstantFormula(2));
_spatialStrcuture.GlobalMoleculeDependentProperties.Add(_globalParameter);
var topcontainer = new Container().WithName("Organism");
var organ = new Container().WithName("Organ").WithParentContainer(topcontainer);
var mp = new Container().WithName(Constants.MOLECULE_PROPERTIES).WithParentContainer(organ);
new Parameter().WithName("Local").WithFormula(new ConstantFormula(3)).WithParentContainer(mp);
_spatialStrcuture.AddTopContainer(topcontainer);
var neighborhood = new NeighborhoodBuilder().WithName("A2B");
var nmp = new Container().WithName(Constants.MOLECULE_PROPERTIES).WithParentContainer(neighborhood);
new Parameter().WithName("Hallo").WithFormula(new ConstantFormula(4)).WithParentContainer(nmp);
_spatialStrcuture.AddNeighborhood(neighborhood);
}
public void CreateCallableNbhdsTests()
{
var vcfFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "VeryMutated.genome.vcf");
var variantSource = new AlleleReader(vcfFilePath);
var vcfNeighborhood = new VcfNeighborhood(0, "chr1", new VariantSite(123), new VariantSite(125));
List <VcfNeighborhood> VcfNeighborhoods = new List <VcfNeighborhood>()
{
vcfNeighborhood
};
//Test 1, genome is NULL
var neighborhoodBuilder = new NeighborhoodBuilder(new PhasableVariantCriteria(), new VariantCallingParameters(),
variantSource, null, 20);
var neighborhoods = neighborhoodBuilder.ConvertToCallableNeighborhoods(VcfNeighborhoods);
Assert.Equal(1, neighborhoods.Count());
Assert.Equal(2, neighborhoods.First().VcfVariantSites.Count());
Assert.Equal("chr1", neighborhoods[0].ReferenceName);
Assert.Equal("RRR", neighborhoods[0].NbhdReferenceSequenceSubstring);
//Test 2, genome is exists, but doesnt have the right chr
var genomePath = Path.Combine(TestPaths.SharedGenomesDirectory, "Bacillus_cereus", "Sequence", "WholeGenomeFasta");
var refName = "chr_wrong";
Genome genome = new Genome(genomePath, new List <string>()
{
refName
});
ChrReference chrReference = genome.GetChrReference(refName);
neighborhoodBuilder = new NeighborhoodBuilder(new PhasableVariantCriteria(), new VariantCallingParameters(),
variantSource, genome, 20);
neighborhoods = neighborhoodBuilder.ConvertToCallableNeighborhoods(VcfNeighborhoods);
Assert.Equal(1, neighborhoods.Count());
Assert.Equal(2, neighborhoods.First().VcfVariantSites.Count());
Assert.Equal("chr1", neighborhoods[0].ReferenceName);
Assert.Equal("RRR", neighborhoods[0].NbhdReferenceSequenceSubstring);
//Test 3, genome is exists, and DOES have the right chr
refName = "chr";
genome = new Genome(genomePath, new List <string>()
{
refName
});
chrReference = genome.GetChrReference(refName);
neighborhoodBuilder = new NeighborhoodBuilder(new PhasableVariantCriteria(), new VariantCallingParameters(),
variantSource, genome, 20);
vcfNeighborhood = new VcfNeighborhood(0, "chr", new VariantSite(123), new VariantSite(125));
VcfNeighborhoods = new List <VcfNeighborhood>()
{
vcfNeighborhood
};
neighborhoods = neighborhoodBuilder.ConvertToCallableNeighborhoods(VcfNeighborhoods);
Assert.Equal(1, neighborhoods.Count());
Assert.Equal(2, neighborhoods.First().VcfVariantSites.Count());
Assert.Equal("chr", neighborhoods[0].ReferenceName);
Assert.Equal("TAT", neighborhoods[0].NbhdReferenceSequenceSubstring);
}
