tests/testthat/test-tabix.R

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

context("Tabix files manipulation")

bin.df =  data.frame(chr=sample(1:21,1e3, replace=TRUE), start=seq(1,1e5,100), end=seq(99,99999,100))
bin.df = bin.df[order(as.character(bin.df$chr), bin.df$start),]

b1.df = cbind(bin.df, bc=rnorm(nrow(bin.df)))
b2.df = cbind(bin.df, bc=rnorm(nrow(bin.df)), bc2=rnorm(nrow(bin.df)))

test_that("Writes and reads entire files",{
  write.table(b1.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  write.table(b2.df, file="test2.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files(c("test.tsv","test2.tsv"))), 2)
  df = read.bedix("test.tsv.bgz")
  expect_equal(df$bc, b1.df$bc)
  expect_equal(df$chr, b1.df$chr)
  expect_equal(df$start, b1.df$start)
  expect_equal(file.remove(c("test.tsv.bgz","test2.tsv.bgz","test.tsv.bgz.tbi","test2.tsv.bgz.tbi")), rep(TRUE,4))
})

test_that("Removes temporary files or not",{
  write.table(b1.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv", rm.input=FALSE)), 1)
  expect_equal(file.exists("test.tsv"), TRUE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  expect_equal(file.exists("test.tsv"), FALSE)
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
})

test_that("Reads subsets",{
  write.table(b1.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  ii = sort(sample.int(10))
  df = read.bedix("test.tsv.bgz", b1.df[ii,])
  expect_equal(df$bc, b1.df$bc[ii])
  expect_equal(df$chr, b1.df$chr[ii])
  expect_equal(df$start, b1.df$start[ii])
  ii = sort(sample.int(100))
  df = read.bedix("test.tsv.bgz", b1.df[ii,])
  expect_equal(df$bc, b1.df$bc[ii])
  expect_equal(df$chr, b1.df$chr[ii])
  expect_equal(df$start, b1.df$start[ii])
  ii = sort(sample.int(500))
  df = read.bedix("test.tsv.bgz", b1.df[ii,])
  expect_equal(df$bc, b1.df$bc[ii])
  expect_equal(df$chr, b1.df$chr[ii])
  expect_equal(df$start, b1.df$start[ii])
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
})

test_that("Bins are ordered",{
  write.table(b1.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  ii = sample.int(100)
  df = read.bedix("test.tsv.bgz", b1.df[ii,])
  expect_equal(order(as.character(df$chr), df$start), 1:nrow(df))
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
})

test_that("Reads files with multiple columns",{
  write.table(b2.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  df = read.bedix("test.tsv.bgz")
  expect_equal(df$bc, b2.df$bc)
  expect_equal(df$bc2, b2.df$bc2)
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
})

test_that("reads file with or without headers",{
  write.table(b2.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  expect_equal(nrow(read.bedix("test.tsv.bgz")), nrow(b2.df))
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
  write.table(b2.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE, col.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  expect_equal(nrow(read.bedix("test.tsv.bgz", header=FALSE)), nrow(b2.df))
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
})

test_that("reads file with or without .bgz extension",{
  write.table(b2.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  expect_equal(file.exists("test.tsv"), FALSE)
  expect_equal(nrow(read.bedix("test.tsv")), nrow(b2.df))
  expect_equal(nrow(read.bedix("test.tsv.bgz")), nrow(b2.df))
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
})

test_that("Checks that files exists",{
  write.table(b2.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_error(comp.index.files(c("test.tsv", "fakefile.tsv")), "file not found")
  expect_error(read.bedix("fakefile.tsv"), "file not found")
  expect_equal(length(comp.index.files("test.tsv")), 1)
  file.remove("test.tsv.bgz.tbi")
  expect_error(read.bedix("test.tsv.bgz"), "file not found")
  file.remove("test.tsv.bgz")
})

test_that("Checks for bins missing columns",{
  write.table(b1.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  bad.df = bin.df[,c("chr","start")]
  expect_error( read.bedix("test.tsv.bgz", bad.df), "Missing column")
  bad.df = bin.df[,c("end","start")]
  expect_error( read.bedix("test.tsv.bgz", bad.df), "Missing column")
  bad.df = bin.df[,c("chr","end")]
  expect_error( read.bedix("test.tsv.bgz", bad.df), "Missing column")
  good.df = bin.df[,c("chr","end", "start")]
  expect_equal(nrow(read.bedix("test.tsv", good.df)), nrow(good.df))
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
})

test_that("Returns null if no data in the queried region", {
  write.table(b1.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  b1.df = b1.df[sort(sample.int(nrow(b1.df), 10)),]
  b1.df$chr = 22
  df = read.bedix("test.tsv.bgz", b1.df)
  expect_true(is.null(df))
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
})

test_that("Factors doesn't cause errors",{
  write.table(b1.df, file="test.tsv", quote=FALSE, sep="\t", row.names=FALSE)
  expect_equal(length(comp.index.files("test.tsv")), 1)
  ii = sort(sample.int(10))
  df = read.bedix(factor("test.tsv.bgz"), b1.df[ii,])
  expect_equal(df$bc, b1.df$bc[ii])
  expect_equal(df$chr, b1.df$chr[ii])
  expect_equal(df$start, b1.df$start[ii])
  file.remove("test.tsv.bgz","test.tsv.bgz.tbi")
})