tests/testthat/test-gencode.R

In LieberInstitute/GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode

txdb_v31_hg19_chr21 <- gencode_txdb("31", "hg19", chrs = "chr21")
txdb_v31_hg19_chr21_disk <- AnnotationDbi::loadDb(
    system.file("extdata", "txdb_v31_hg19_chr21.sqlite",
        package = "GenomicState"
    )
)
genes_v31_hg19_chr21 <- gencode_annotated_genes(txdb_v31_hg19_chr21)
gs_v31_hg19_chr21 <- gencode_genomic_state(txdb_v31_hg19_chr21)

test_that("Gencode genomic states", {
    expect_equal(
        gencode_source_url(version = "31", genome = "hg19"),
        "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/GRCh37_mapping/gencode.v31lift37.annotation.gtf.gz"
    )
    expect_equal(
        gencode_source_url(version = "31", genome = "hg38"),
        "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/gencode.v31.annotation.gtf.gz"
    )

    expect_equivalent(txdb_v31_hg19_chr21, txdb_v31_hg19_chr21_disk)
    expect_equal(
        unique(seqnames(genes_v31_hg19_chr21)),
        factor("chr21")
    )
    expect_equal(
        any(grepl("\\.", genes_v31_hg19_chr21$Geneid)),
        FALSE
    )
    expect_equal(length(genes_v31_hg19_chr21), 823)

    ## Same gene symbols are used
    expect_equal(
        sort(unique(genes_v31_hg19_chr21$Gene)),
        sort(unique(unlist(gs_v31_hg19_chr21$fullGenome$symbol)))
    )
    expect_equal(
        sort(unique(genes_v31_hg19_chr21$Gene)),
        sort(unique(unlist(gs_v31_hg19_chr21$codingGenome$symbol)))
    )
})