tests/testthat/test_get_transcriptome_seq_from_transcriptome_id.R

In avidaR: A Computational Biologist’s Toolkit To Get Data From 'avidaDB'

test_that("get_transcriptome_seq_from_transcriptome_id", {
  
  skip_if_offline(host = "graphdb.fortunalab.org")
  
  suppressMessages({
    triplestore <- triplestore_access$new()
    
    response <- triplestore$set_access_options(
      url = "https://graphdb.fortunalab.org",
      user = "public_avida",
      password = "public_avida",
      repository = "avidaDB_test"
    )
    
    found1 <- get_transcriptome_seq_from_transcriptome_id(
      transcriptome_id = 53674,
      triplestore = triplestore
    )
  
    found2 <- get_transcriptome_seq_from_transcriptome_id(
      transcriptome_id = c(53674, 1666099),
      seed_id = c(2,1),
      transcriptome_pos = TRUE,
      triplestore = triplestore
    )
  
    found3 <- get_transcriptome_seq_from_transcriptome_id(
      transcriptome_id = 53674,
      genome_seq = TRUE,
      triplestore = triplestore
    )
    
    skip_if(is.null(response) || is.null(found1) || is.null(found2) || is.null(found3))
  
    expect_match(class(found1), "data.frame")
    expect_equal(nrow(found1), 1)
    expect_equal(colnames(found1), c("transcriptome_id", "transcriptome_seq"))
  
    expect_match(class(found2), "data.frame")
    expect_true(nrow(found2) > 0)
    expect_equal(colnames(found2), c("seed_id", "transcriptome_id", "transcriptome_seq", "transcriptome_pos"))
    expect_equal(grepl("|", found2$transcriptome_pos[1]), TRUE)
  
    expect_match(class(found3), "data.frame")
    expect_equal(nrow(found3), 1)
    expect_equal(colnames(found3), c("transcriptome_id", "transcriptome_seq", "genome_seq"))
    expect_equal(found3$genome_seq[1], "eirlxtxqauwatcknjayqgcufvylzdjpokplcvbzamnyyfqesoktrvxgauuqfufmjszbzwtdunnpvfmpplfuuvcmpvyftkgvxxhpp")
    expect_equal(nchar(found3$transcriptome_seq[1]), 1490)    
  })
  
})