tests/testthat/test_find_novel_exons.R

In khembach/DISCERNS: DISCovery of unannotated Exons from RNa-seq Splice junction reads

context("Predict novel exons")

library(DISCERNS)

gtf <- system.file("extdata", "selected.gtf", package = "DISCERNS", 
                   mustWork = TRUE)
anno <- prepare_annotation(gtf)

sj <- system.file("extdata", "selected.SJ.out.tab", 
                  package = "DISCERNS", mustWork = TRUE)
bam <- system.file("extdata", "selected.bam", 
                   package = "DISCERNS", mustWork = TRUE)


novel_exon_df <- find_novel_exons(sj_filename = sj, annotation = anno, 
                                  min_unique = 1, bam = bam)

test_that("output from find_novel_exons is correct", {
  expect_s3_class(novel_exon_df, "data.frame")
  expect_equal(ncol(novel_exon_df), 10)
  expect_equal(colnames(novel_exon_df), c("seqnames", "lend", "start", "end", 
                                          "rstart", "strand", "unique_left", 
                                          "unique_right", "min_reads", "ID"))
  expect_s3_class(novel_exon_df$seqnames, "factor")
  expect_type(novel_exon_df$start, "integer")
  expect_type(novel_exon_df$end, "integer")
  expect_s3_class(novel_exon_df$strand, "factor")
  expect_type(novel_exon_df$lend, "integer")
  expect_type(novel_exon_df$rstart, "integer")
  expect_type(novel_exon_df$unique_left, "integer")
  expect_type(novel_exon_df$unique_right, "integer")
  expect_type(novel_exon_df$min_reads, "integer")
  expect_type(novel_exon_df$ID, "integer")
})

test_that("parameters work", {
  ## The parameters should not be <= 0
  expect_error(find_novel_exons(sj_filename = sj, annotation = anno, 
                                min_unique = 1, bam = bam, read_length = -100))
  expect_error(find_novel_exons(sj_filename = sj, annotation = anno, 
                                min_unique = 1, bam = bam, overhang_min = -12))
  expect_error(find_novel_exons(sj_filename = sj, annotation = anno, 
                                min_unique = 1, bam = bam, 
                                min_intron_size = -21))
})