tests/testthat/test-sort.region.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('bedr.sort.region')


test_that('bedr.sort.region handles parameter input', {	
	if (check.binary('bedtools', verbose = TRUE)) {
		regions <- get.example.regions();
		region.a.sorted.lex <- c('chr1:10-100', 'chr1:101-200', 'chr1:200-210', 'chr1:211-212', 'chr10:50-100', 'chr2:10-50',   'chr2:40-60', 'chr20:1-5');
		region.a.sorted.nat <- c('chr1:10-100', 'chr1:101-200', 'chr1:200-210', 'chr1:211-212', 'chr2:10-50',   'chr2:40-60','chr10:50-100', 'chr20:1-5');

		# garbage parameters
		expect_error(bedr.sort.region(regions$a, method = 'xxx', engine = 'unix', verbose = FALSE));
		expect_error(bedr.sort.region(regions$a, method = 'lexicographical', engine = 'xxx', verbose = FALSE));

		# bad region
		expect_error(bedr.sort.region(regions$d, verbose = FALSE));

		# string (index) vs dataframe
		expect_equal(bedr.sort.region(regions$a, verbose = FALSE), region.a.sorted.lex);

		expect_error(bedr.sort.region(as.data.frame(regions$a), verbose = FALSE)); # b/c it's a factor
		#expect_equivalent(bedr.sort.region(data.frame(index = regions$a, stringsAsFactors=FALSE), verbose = FALSE), as.data.frame(region.a.sorted.lex, stringsAsFactors = FALSE));
		expect_equal(bedr.sort.region(data.frame(index = regions$a, stringsAsFactors=FALSE), verbose = FALSE), as.data.frame(region.a.sorted.lex, stringsAsFactors = FALSE), ignore_attr = TRUE);

		# index vs bed format
		region.a.matrix.sorted <- as.matrix(index2bed(region.a.sorted.lex));
		region.a.df <- as.data.frame(index2bed(regions$a), stringsAsFactors = FALSE);
		region.a.df.sorted <- as.data.frame(index2bed(region.a.sorted.lex), stringsAsFactors = FALSE, row.names = region.a.sorted.lex);
		expect_error(bedr.sort.region(region.a.matrix, verbose = FALSE)); # matrix / string conversion messes up regions 
		#expect_equivalent(bedr.sort.region(region.a.df, verbose = FALSE), region.a.df.sorted);
		expect_equal(bedr.sort.region(region.a.df, verbose = FALSE), region.a.df.sorted, ignore_attr = TRUE);

		# verbose returns
		}
	});
test_that('bedr.sort.region correctly does lexicographical sorting', {
	if (check.binary('bedtools', verbose = TRUE)) {
		regions <- get.example.regions();
		region.a.sorted.lex <- c('chr1:10-100', 'chr1:101-200', 'chr1:200-210', 'chr1:211-212', 'chr10:50-100', 'chr2:10-50',   'chr2:40-60', 'chr20:1-5');

		# unix
		expect_equal(bedr.sort.region(regions$a, method = 'lexicographical', engine = 'unix', verbose = FALSE), region.a.sorted.lex);
		# R
		expect_equal(bedr.sort.region(regions$a, method = 'lexicographical', engine = 'R', verbose = FALSE), region.a.sorted.lex);
		# bedtools
		expect_equal(bedr.sort.region(regions$a, method = 'lexicographical', engine = 'bedtools', verbose = FALSE), region.a.sorted.lex);
		if (check.binary('bedops', verbose = FALSE)) {
	  # bedops
		expect_equal(bedr.sort.region(regions$a, method = 'lexicographical', engine = 'bedops', verbose = FALSE), region.a.sorted.lex);
		}
		}
	});
test_that('bedr.sort.region correctly does natural sorting', {
	if (check.binary('bedtools', verbose = TRUE)) {
		regions <- get.example.regions();
		region.a.sorted.nat <- c('chr1:10-100', 'chr1:101-200', 'chr1:200-210', 'chr1:211-212','chr2:10-50', 'chr2:40-60', 'chr10:50-100', 'chr20:1-5');

		# unix
		expect_equal(bedr.sort.region(regions$a, method = 'natural', engine = 'unix', verbose = FALSE), region.a.sorted.nat);
		# R
		expect_equal(bedr.sort.region(regions$a, method = 'natural', engine = 'R', verbose = FALSE), region.a.sorted.nat);
		# bedtools
		expect_equal(bedr.sort.region(regions$a, method = 'natural', engine = 'bedtools', verbose = FALSE), region.a.sorted.nat);
		if (check.binary('bedops', verbose = FALSE)) {
	  # bedops
		expect_equal(bedr.sort.region(regions$a, method = 'natural', engine = 'bedops', verbose = FALSE), region.a.sorted.nat);
		}
	  }
	})