inst/tests/test.process.input.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)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
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context("process.input")

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

	test_that("check input processing i.e. converting to bed and sending to a tmp file", {
	
		regions <- get.example.regions()
		regions$a <- bedr.sort.region(regions$a)

		# good region
		expect_equal(length(process.input(regions$a, verbose = F)), 1);
		expect_equal(attributes(process.input(regions$a, verbose = F)[[1]]), list(is.index=T,is.file=F));
	
		expect_equal(length(process.input(index2bed(regions$a), verbose = F)), 1);
		expect_equal(attributes(process.input(index2bed(regions$a), verbose = F)[[1]]), list(is.index=F,is.file=F));
	
		expect_equal(length(process.input("chrY:24052505-24052506", verbose = F)), 1);
		expect_equal(attributes(process.input("chrY:24052505-24052506", verbose = F)[[1]]), list(is.index=T,is.file=F));


		})

}