tests/testthat/test_longSeq.r

In coil: Contextualization and Evaluation of COI-5P Barcode Data

test_that("A long sequence is framed and translated properly", {
  #can the program pull off the folmer primers?
  f_front = 'GGTCAACAAATCATAAAGATATTGG'
  ex_seq = "ctctacttgatttttggtgcatgagcaggaatagttggaatagctttaagtttactaattcgcgctgaactaggtcaacccggatctcttttaggggatgatcagatttataatgtgatcgtaaccgcccatgcctttgtaataatcttttttatggttatacctgtaataattggtggctttggcaattgacttgttcctttaataattggtgcaccagatatagcattccctcgaataaataatataagtttctggcttcttcctccttcgttcttacttctcctggcctccgcaggagtagaagctggagcaggaaccggatgaactgtatatcctcctttagcaggtaatttagcacatgctggcccctctgttgatttagccatcttttcccttcatttggccggtatctcatcaattttagcctctattaattttattacaactattattaatataaaacccccaactatttctcaatatcaaacaccattatttgtttgatctattcttatcaccactgttcttctactccttgctctccctgttcttgcagccggaattacaatattattaacagaccgcaacctcaacactacattctttgaccccgcagggggaggggacccaattctctatcaacactta"
  f_rear = 'TAAACTTCAGGGTGACCAAAAAATCA'

  folmer_test = coi5p_pipe(paste0(f_front,ex_seq, f_rear ), name = 'primer_test')

  #26th bp is bp 1, the 25 primer bp are removed - removes 24/25 primer bases
  expect_equal(folmer_test$data$raw_start, 25)
  expect_equal(nchar(folmer_test$framed)-3, nchar(ex_seq))

  sequence = 'aaccgctgattattttcaaccaaccacaaagatatcggcaaactttatattttatttttggagcttgagctggaatagttggaacatctttaagaattttaattcgagctgaattaggacatcctggagcattaattggagatgatcaaatttataatgtaattgtaactgcacatgcttttattataattttttttatggttatacctattataattggtggatttggaaattgattagtgcctttaatattaggtgctcctgatatagcattcccacgaataaataatataagattttgactactacctcctgctctttctttactattagtaagtagaatagttgaaaatggagctggaacaggatgaactgtttatccacctttatccgctggaattgctcatggtggagcttcagttgatttagctattttttctctacatttagcagggatttcttcaattttaggagctctaaattttattacaactgtaattaatatacgatcaacaggaatttcattagatcgtatacctttatttgtttgatcagtagttattactgctttattattgttattatcacttccagtactagcaggagctattactatattattaacagatcgaaatttaaatacatcattttttgacccagcgggaggaggagatcctattttatatcaacatttattatttattta'
  sequence_framed = 'actttatattttatttttggagcttgagctggaatagttggaacatctttaagaattttaattcgagctgaattaggacatcctggagcattaattggagatgatcaaatttataatgtaattgtaactgcacatgcttttattataattttttttatggttatacctattataattggtggatttggaaattgattagtgcctttaatattaggtgctcctgatatagcattcccacgaataaataatataagattttgactactacctcctgctctttctttactattagtaagtagaatagttgaaaatggagctggaacaggatgaactgtttatccacctttatccgctggaattgctcatggtggagcttcagttgatttagctattttttctctacatttagcagggatttcttcaattttaggagctctaaattttattacaactgtaattaatatacgatcaacaggaatttcattagatcgtatacctttatttgtttgatcagtagttattactgctttattattgttattatcacttccagtactagcaggagctattactatattattaacagatcgaaatttaaatacatcattttttgacccagcgggaggaggagatcctattttatatcaacattta'

  sequence_AAcensored = "TLYFIFGAWAG?VGTSL?ILIRAELGHPGALIGDDQIYNVIVTAHAFI?IFFMV?PI?IGGFGNWLVPL?LGAPD?AFPR?NN??FWLLPPALSLLLVS??VENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGALNFITTVIN?RSTGISLDR?PLFVWSVVITALLLLLSLPVLAGAIT?LLTDRNLNTSFFDPAGGGDPILYQHL"
  sequence_AA5 = "TLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGALNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHL"

  dat = coi5p(sequence)
  expect_equal(dat$raw, sequence)
  expect_identical(dat$name, character(0))

  dat = frame(dat)
  expect_equal(dat$framed, sequence_framed)

  dat = translate(dat)
  expect_equal(dat$aaSeq, sequence_AAcensored)

  dat = indel_check(dat)
  expect_equal(dat$indel_likely, FALSE)
  expect_equal(dat$stop_codons, FALSE)

  dat = translate(dat, trans_table = 5)
  expect_equal(dat$aaSeq, sequence_AA5)

  dat = indel_check(dat)
  expect_equal(dat$indel_likely, FALSE)
  expect_equal(dat$stop_codons, FALSE)

})