tests/testthat/test-fetch_sequences_from_protein_ids.R

In richelbilderbeek/sprentrez: Do Big Rentrez Queries

test_that("use", {
  Sys.sleep(1)

  protein_ids <- c(
    "NP_009089.4",
    "NP_001007554.1",
    "NP_001123995.1",
    "NP_001229820.1",
    "NP_001229821.1",
    "NP_001229822.1"
  )
  sequences <- fetch_sequences_from_protein_ids(protein_ids = protein_ids)
  expect_equal(
    length(sequences),
    length(protein_ids)
  )
  regexp <- paste0(
    "[",
    paste0(Peptides::aaList(), collapse = ""),
    "]+"
  )
  expect_equal(
    length(protein_ids),
    sum(stringr::str_count(sequences, regexp))
  )
})

test_that("verbose error", {
  Sys.sleep(1)
  expect_error(
    fetch_sequences_from_protein_ids(
      protein_ids = "NP_123.4",
    )
  )
})

test_that("Large requests are handled nicely as well", {
  Sys.sleep(1)
  protein_ids_filename <- system.file(
    "extdata", "protein_ids.csv", package = "sprentrez"
  )
  protein_ids <- readr::read_csv(
    file = protein_ids_filename,
    col_types = readr::cols(protein_id = readr::col_character())
  )$protein_id
  sequences <- fetch_sequences_from_protein_ids(protein_ids = protein_ids)
  expect_equal(0, sum(is.na(sequences)))
})