tests/testthat/test-TxDb.R

In arendsee/fagin: Annotate Orphan Genes

context("TxDb")

gff <- system.file("yeast", "gff", "Saccharomyces_paradoxus.gff", package='fagin')
dna <- system.file("yeast", "fna", "Saccharomyces_paradoxus.fna", package='fagin')

genomeDB <- load_dna(dna)
seqinfo <- GenomicFeatures::seqinfo(genomeDB)

# hold gene models Rmonad object 
m_gffDB <- NULL
gffDB <- NULL 

test_that("load gene models", {
  expect_silent({
    m_gffDB <<- load_gene_models(gff, seqinfo)
    gffDB <<- rmonad::get_value(m_gffDB, m_gffDB@head)[[1]]
  })
  expect_true(all(rmonad::get_OK(m_gffDB)))
  expect_equal(rmonad::get_value(m_gffDB, m_gffDB@head)[[1]] %>% top_class, "TxDb")
})

test_that("summarization doesn't explode", {
  expect_true(all(m_gffDB %>>% summarize_gff %>% rmonad::get_OK())) 
})

gffsum <- m_gffDB %>>% summarize_gff %>% rmonad::get_value(., .@head)
gffsum <- gffsum[[1]]

test_that("summarization is good", {
  expect_equal(top_class(gffsum), "gff_summary")
})

m_prots <- NULL
test_that("m_get_proteins works", {
  expect_true({
    m_prots <<- m_get_proteins(
      gffDB        = gffDB,
      genomeDB     = genomeDB,
      species_name = "Saccharomyces_paradoxus"
    )
    rmonad::get_OK(m_prots, m_prots@head)
  })
})

grlist <- rmonad::get_value(m_prots, tag='cdsRangeList')[[1]]
test_that("trim_CDS_with_non_zero_phase", {
  expect_equal(class(grlist), class(trim_CDS_with_non_zero_phase(grlist))) 
  expect_equal(names(grlist), names(trim_CDS_with_non_zero_phase(grlist))) 
})

phases <- NULL
test_that("phase summaries are proper", {
  expect_silent(
    phases <<- rmonad::funnel(
      phases = rmonad::view(m_prots, "aa_model_phase/Saccharomyces_paradoxus"),
      aa = rmonad::view(m_prots, "faa/Saccharomyces_paradoxus")
    ) %*>%
    summarize_phase
  )
})