public void GetColumnIndices_missing_column()
{
const string header = @"CNV_ID ID_GENE gene_name ID_SAMPLE ID_TUMOUR Primary site Site subtype 1 Site subtype 2 Site subtype 3 Primary histology Histology subtype 1 Histology subtype 2 Histology subtype 3 SAMPLE_NAME TOTAL_CN MINOR_ALLELE MUT_TYPE ID_STUDY Chromosome:G_Start..G_Stop";
var readStream = ResourceUtilities.GetReadStream(Resources.SaPath("CosmicCNV.tsv"));
var cnvReader = new CosmicCnvReader(readStream,
ChromosomeUtilities.RefNameToChromosome,
GenomeAssembly.GRCh37);
Assert.Throws <InvalidDataException>(() => cnvReader.GetColumnIndices(header));
}
public void GetEntries()
{
var readStream = ResourceUtilities.GetReadStream(Resources.SaPath("CosmicCNV.tsv"));
var cnvReader = new CosmicCnvReader(readStream,
ChromosomeUtilities.RefNameToChromosome,
GenomeAssembly.GRCh37);
var cnvItems = cnvReader.GetEntries();
Assert.Equal(5, cnvItems.Count());
}
public void GetColumnIndices_valid_header()
{
const string header = @"CNV_ID ID_GENE gene_name ID_SAMPLE ID_TUMOUR Primary site Site subtype 1 Site subtype 2 Site subtype 3 Primary histology Histology subtype 1 Histology subtype 2 Histology subtype 3 SAMPLE_NAME TOTAL_CN MINOR_ALLELE MUT_TYPE ID_STUDY GRCh Chromosome:G_Start..G_Stop";
var readStream = ResourceUtilities.GetReadStream(Resources.SaPath("CosmicCNV.tsv"));
var cnvReader = new CosmicCnvReader(readStream,
ChromosomeUtilities.RefNameToChromosome,
GenomeAssembly.GRCh37);
cnvReader.GetColumnIndices(header);
//we do not need an assert because not getting an exception in the last line means pass
}
public void GetColumnIndices_missing_column()
{
var header = @"CNV_ID ID_GENE gene_name ID_SAMPLE ID_TUMOUR Primary site Site subtype 1 Site subtype 2 Site subtype 3 Primary histology Histology subtype 1 Histology subtype 2 Histology subtype 3 SAMPLE_NAME TOTAL_CN MINOR_ALLELE MUT_TYPE ID_STUDY Chromosome:G_Start..G_Stop";
var readStream = ResourceUtilities.GetReadStream(Resources.TopPath("SA\\CosmicCNV.tsv"));
var cnvReader = new CosmicCnvReader(readStream,
new Dictionary <string, IChromosome>()
{
{ "W", new Chromosome("chrW", "W", 1) }
},
GenomeAssembly.GRCh37);
Assert.Throws <InvalidDataException>(() => cnvReader.GetColumnIndices(header));
}
public void GetEntries()
{
var readStream = ResourceUtilities.GetReadStream(Resources.TopPath("SA\\CosmicCNV.tsv"));
var cnvReader = new CosmicCnvReader(readStream,
new Dictionary <string, IChromosome>()
{
{ "17", new Chromosome("chr17", "17", 1) },
{ "Y", new Chromosome("chrY", "Y", 2) },
{ "MT", new Chromosome("chrM", "MT", 3) }
},
GenomeAssembly.GRCh37);
var cnvItems = cnvReader.GetEntries();
Assert.Equal(5, cnvItems.Count());
}
