inst/tests/test.convert2bed.R

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

# The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
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context("convert2bed")

if (check.binary("bedtools", verbose = TRUE)) {

	test_that("check converting a region into bed file including file type checking and region verification", {
	
		regions <- get.example.regions()
		regions$a <- bedr.sort.region(regions$a)
		regions$b <- bedr.sort.region(regions$b)
		a.bed <- index2bed(regions$a)
		b.bed <- index2bed(regions$b)

		# bad region
		expect_error(convert2bed("meow", verbose = F))

		# good region
		expect_equivalent(convert2bed(regions$a, verbose = F), a.bed);
		expect_equivalent(convert2bed(regions$b, verbose = F), b.bed);
		expect_equivalent(convert2bed("chrY:24052505-24052506", verbose = F), data.frame(chr="chrY", start=24052505, end=24052506, stringsAsFactors = FALSE));


		})
}