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 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)); }