context("test-annotate")
test_that("annotate works", {
variants.bed <- read.table(text=
"chr1 100 200 nasty 1 -
chr2 500 1000 ugly 2 +
chr3 1000 5000 big 3 -")
genes.bed <- read.table(text=
"chr1 150 200 geneA 1 +
chr1 175 250 geneB 2 +
chr3 0 10000 geneC 3 -")
conserve.bed <- read.table(text=
"chr1 0 10000 cons1 1 +
chr2 700 10000 cons2 2 -
chr3 4000 10000 cons3 3 +")
known_var.bed <- read.table(text=
"chr1 0 120 known1 -
chr1 150 160 known2 -
chr2 0 10000 known3 +")
results <- read.table(text=
"chr1 100 200 nasty 1 - 0.500000 1.000000 0.300000
chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000
chr3 1000 5000 big 3 - 1.000000 0.250000 0.000000")
expect_equal(bedtoolsr::bt.annotate(variants.bed, list(genes.bed, conserve.bed, known_var.bed)), results)
})
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