tests/testthat-extra/test-ensembl.R

In acidgenomics/freerange: Generate and Manipulate Genomic Ranges

context("Ensembl annotations")

mat <- .ucscMatrix
keep <- as.logical(mat[, "ensembldb"])
mat <- mat[keep, , drop = FALSE]

## Note that we're running at transcript level here to check the gene merge.
##
## Potential issues:
## - *Caenorhabditis elegans*
##     - Invalid transcript IDs.
## - *Canis familiaris*
##     - Using the full *Canis lupus familiaris* won't match.
## - *Saccharomyces cerevisiae*
##     - Invalid gene IDs.
##     - Iinvalid transcript IDs.
##     - No gene names.

with_parameters_test_that(
    "UCSC genome build remaps", {
        object <- makeGRangesFromEnsembl(
            organism = organism,
            genomeBuild = genomeBuild,
            level = "transcripts"
        )
        expect_s4_class(object, "GRanges")
    },
    organism = mat[, "organism"],
    genomeBuild = mat[, "ucsc"]
)