tests/testthat/test_query.r

In MRCIEU/gwasvcf: Tools for Dealing with GWAS Summary Data in VCF Format

context("Querying vcf files")
library(gwasvcf)


fn <- system.file("extdata","data.vcf.gz", package="gwasvcf")
vcf <- VariantAnnotation::readVcf(fn)



test_that("query_gwas", {
	chrompos<- c("1:800000-1000000")
	rsid <- c("rs3128126", "rs3121561", "rs3813193")
	id <- "IEU-a-2"
	pval <- 0.2

	expect_true({
		a = query_gwas(fn, chrompos=chrompos, os="Darwin")
		b = query_gwas(fn, chrompos=chrompos, os="Windows")
		c = query_gwas(fn, chrompos=chrompos, id=id, os="Darwin")
		d = query_gwas(fn, chrompos=chrompos, id=id, os="Windows")
		all(a == b) && all(b == c) && all(c == d)
	})

	expect_true({
		a = query_gwas(fn, rsid=rsid, os="Darwin")
		b = query_gwas(fn, rsid=rsid, os="Windows")
		c = query_gwas(fn, rsid=rsid, id=id, os="Darwin")
		d = query_gwas(fn, rsid=rsid, id=id, os="Windows")
		all(a == b) && all(b == c) && all(c == d)
	})

	expect_true({
		a = query_gwas(fn, pval=pval, os="Darwin")
		b = query_gwas(fn, pval=pval, os="Windows")
		c = query_gwas(fn, pval=pval, id=id, os="Darwin")
		d = query_gwas(fn, pval=pval, id=id, os="Windows")
		all(a == b) && all(b == c) && all(c == d)
	})

	expect_true({
		a = query_gwas(vcf, chrompos=chrompos, os="Darwin")
		b = query_gwas(vcf, chrompos=chrompos, os="Windows")
		c = query_gwas(vcf, chrompos=chrompos, id=id, os="Darwin")
		d = query_gwas(vcf, chrompos=chrompos, id=id, os="Windows")
		all(a == b) && all(b == c) && all(c == d)
	})

	expect_true({
		a = query_gwas(vcf, rsid=rsid, os="Darwin")
		b = query_gwas(vcf, rsid=rsid, os="Windows")
		c = query_gwas(vcf, rsid=rsid, id=id, os="Darwin")
		d = query_gwas(vcf, rsid=rsid, id=id, os="Windows")
		all(a == b) && all(b == c) && all(c == d)
	})

	expect_true({
		a = query_gwas(vcf, pval=pval, os="Darwin")
		b = query_gwas(vcf, pval=pval, os="Windows")
		c = query_gwas(vcf, pval=pval, id=id, os="Darwin")
		d = query_gwas(vcf, pval=pval, id=id, os="Windows")
		all(a == b) && all(b == c) && all(c == d)
	})
})


test_that("parse_chrompos", {
	expect_equal(parse_chrompos("1:10000") %>% length, 1)
	expect_equal(parse_chrompos("1:10000-100000") %>% length, 1)
	expect_equal(parse_chrompos(c("1:10000-10000", "2:100-200")) %>% length, 2)
	expect_equal(parse_chrompos(dplyr::tibble(chrom=c(1,2),start=c(10000,100), end=c(10000,200))) %>% length, 2)
})


test_that("vcf_to_granges", {
	g <- vcf_to_granges(vcf)
	expect_equal(length(g), length(vcf))
})


test_that("query_chrompos_file", {
	g <- parse_chrompos("1:800000-1000000")
	v <- query_chrompos_file(g, fn)
	expect_equal(length(v), 3)
})


test_that("query_rsid_file", {
	v <- query_rsid_file(c("rs3128126", "rs3121561", "rs3813193"), fn)
	expect_equal(length(v), 3)
})


test_that("query_pval_file", {
	v <- query_pval_file(0.2, fn)
	expect_true(length(v) < 92)
	expect_true(length(v) > 5)
})


test_that("query_chrompos_vcf", {
	v <- query_chrompos_vcf("1:800000-1000000", vcf)
	expect_equal(length(v), 3)
})


test_that("query_rsid_vcf", {
	v <- query_rsid_vcf(c("rs3128126", "rs3121561", "rs3813193"), vcf)
	expect_equal(length(v), 3)
})


test_that("query_pval_vcf", {
	v <- query_pval_vcf(0.2, vcf)
	expect_true(length(v) < 92)
	expect_true(length(v) > 5)
})


test_that("query_rsid_bcftools", {
  skip_on_os("windows")
	set_bcftools()
	v <- query_rsid_bcftools(c("rs3128126", "rs3121561", "rs3813193"), fn)
	expect_equal(length(v), 3)
})


test_that("query_pval_bcftools", {
  skip_on_os("windows")
	set_bcftools()
	v <- query_pval_bcftools(0.2, fn)
	expect_true(length(v) < 92)
	expect_true(length(v) > 5)
})


test_that("query_chrompos_vcf", {
  skip_on_os("windows")
	set_bcftools()
	v <- query_chrompos_bcftools("1:800000-1000000", fn)
	expect_equal(length(v), 3)
})


test_that("query_chrompos_vcf url", {
  skip_on_ci()
  skip_on_os(c("mac", "windows"))
	set_bcftools()
	u <- "https://objectstorage.us-ashburn-1.oraclecloud.com/n/idrvm4tkz2a8/b/OpenGWAS/o/ieu-a/ieu-a-2/ieu-a-2.vcf.gz"
	RCurl::url.exists(u)
	v <- query_chrompos_bcftools("1:800000-1000000", u)
	expect_equal(length(v), 3)
})

test_that("query_chrompos_vcf url2", {
  skip_on_ci()
  skip_on_os(c("mac", "windows"))
	set_bcftools()
	u <- "https://objectstorage.us-ashburn-1.oraclecloud.com/n/idrvm4tkz2a8/b/OpenGWAS/o/ieu-a/ieu-a-2/ieu-a-2.vcf.gz"
	# RCurl::url.exists(u)
	v <- query_gwas(u, "1:800000-1000000")
	expect_equal(length(v), 3)
})

test_that("query_chrompos_vcf url2", {
  skip_on_ci()
  skip_on_os(c("mac", "windows"))
	set_bcftools()
	u <- "https://objectstorage.us-ashburn-1.oraclecloud.com/n/idrvm4tkz2a8/b/OpenGWAS/o/ieu-a/ieu-a-2/ieu-a-2.vcf.gz"
	v <- query_gwas(u, pval=5e-8)
	expect_equal(length(v), 2041)
})