Nothing
test_that("A sequence with a deletion is framed and translated properly", {
sequence = 'accctttacttaatctttggtgcatgagcaggaatagtaggtacagcccttagcttgcttattcgagcagaattaagccaacctggcacactcctgggagacgatcagatctacaatgttatcgtaactgctcacgcttttgtaataattttttttatggttatacctgtaataattggtgggttcggaaactgattagtgcctttaataattggtgcaccggacatagctttcccacgaataaataacataagcttttgactgctacccccctccctcctattacttttggcctctgctggagttgaagccggagccggaactggttgaacagtttatccccccctcgcaagtaatatagcccacgctggggcatcagtagacttagctattttctcgctccatttagcggtatttcctcaattcttgcctctatcaactttattacaaccattattaatataaaaccgcctgccatctctcaatatcaaacacccctttttgtttgatctattcttgtaaccacagtcctactcctcctttcacttcctgttcttgcagccgcaattacaatactacttaccgaccgtaatttaaacacaacattttttgatcctgctggtgggggtgacccaattctttaccaacattta'
sequence_framed = 'accctttacttaatctttggtgcatgagcaggaatagtaggtacagcccttagcttgcttattcgagcagaattaagccaacctggcacactcctgggagacgatcagatctacaatgttatcgtaactgctcacgcttttgtaataattttttttatggttatacctgtaataattggtgggttcggaaactgattagtgcctttaataattggtgcaccggacatagctttcccacgaataaataacataagcttttgactgctacccccctccctcctattacttttggcctctgctggagttgaagccggagccggaactggttgaacagtttatccccccctcgcaagtaatatagcccacgctggggcatcagtagacttagctattttctcgctccatttagcggtatttcctcaattcttgcctctatcaactttattacaaccattattaatataaaaccgcctgccatctctcaatatcaaacacccctttttgtttgatctattcttgtaaccacagtcctactcctcctttcacttcctgttcttgcagccgcaattacaatactacttaccgaccgtaatttaaacacaacattttttgatcctgctggtgggggtgacccaattctttaccaacattta'
sequence_AAcensored = "TLYLIFGAWAG?VGTALSLLIRAELSQPGTLLGDDQIYNVIVTAHAFV?IFFMV?PV?IGGFGNWLVPL?IGAPD?AFPR?NN?SFWLLPPSLLLLLASAGVEAGAGTGWTVYPPLASN?AHAGASVDLAIFSLHLAVFPQFLPLSTLLQPLL??NRLPSLNI?HPFLFDLFL?PQSYSSFHFLFLQPQLQYYLPTVI?TQHFLILLVGVTQFFTNI-"
sequence_AA5 = "TLYLIFGAWAGMVGTALSLLIRAELSQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPVMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSLLLLLASAGVEAGAGTGWTVYPPLASNMAHAGASVDLAIFSLHLAVFPQFLPLSTLLQPLLM*NRLPSLNIKHPFLFDLFL*PQSYSSFHFLFLQPQLQYYLPTVI*TQHFLILLVGVTQFFTNI"
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$indel_likely, TRUE)
expect_equal(dat$stop_codons, FALSE)
dat = translate(dat, trans_table = 5)
expect_equal(dat$aaSeq, sequence_AA5)
dat = indel_check(dat)
expect_equal(dat$indel_likely, TRUE)
expect_equal(dat$stop_codons, TRUE)
})
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