Nothing
test_that("A sequence with missing information is framed and translated properly", {
sequence = 'actttatatctaatttttggggcatgatcagcgatagttggaacagccttnnnnnnnnnnattcgagcagaactaggtcaacctggaagtttaattggagacgaccagatttataatgtgattgttactgcccacgcttttattataattttttttatggttatgcctattataattgggggattcggaaattgacttctacccttaatactaggagctccagatatagcttttccacgtctcaataatataagattttggttattaccccctgccttaatgttattaattagaggatccctagtagaagccggggcgggaactggatggacagtatacccacctctagccagcaatatcgcacnnnnnnnnnnctctgtagacctctctattttttcattacacttagcgggagcttcctctcttttaggagctatcaacttcatatccacagtaattaatatacgagctgaaactttaacattcgaccgtttacctttatttgtatgtagagtatttgtgacggtgattcttctattattatctttacctgtgttagccggagccattactatgcttttaactgaccggaatcttaatacnnnnnttttcgaccctacagggggaggagaccctattttataccaacactta'
sequence_framed = 'actttatatctaatttttggggcatgatcagcgatagttggaacagccttnnnnnnnnnnattcgagcagaactaggtcaacctggaagtttaattggagacgaccagatttataatgtgattgttactgcccacgcttttattataattttttttatggttatgcctattataattgggggattcggaaattgacttctacccttaatactaggagctccagatatagcttttccacgtctcaataatataagattttggttattaccccctgccttaatgttattaattagaggatccctagtagaagccggggcgggaactggatggacagtatacccacctctagccagcaatatcgcacnnnnnnnnnnctctgtagacctctctattttttcattacacttagcgggagcttcctctcttttaggagctatcaacttcatatccacagtaattaatatacgagctgaaactttaacattcgaccgtttacctttatttgtatgtagagtatttgtgacggtgattcttctattattatctttacctgtgttagccggagccattactatgcttttaactgaccggaatcttaatacnnnnnttttcgaccctacagggggaggagaccctattttataccaacactta'
sequence_AAcensored = "TLYLIFGAWSA?VGTA----IRAELGQPGSLIGDDQIYNVIVTAHAFI?IFFMVMPI?IGGFGNWLLPL?LGAPD?AFPRLNN??FWLLPPALMLLI?GSLVEAGAGTGWTVYPPLASNIA----SVDLSIFSLHLAGASSLLGAINF?STVIN?RAETLTFDRLPLFVC?VFVTVILLLLSLPVLAGAITMLLTDRNLN---FDPTGGGDPILYQHL"
sequence_AA5 = "TLYLIFGAWSAMVGTA----IRAELGQPGSLIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLLPLMLGAPDMAFPRLNNMSFWLLPPALMLLISGSLVEAGAGTGWTVYPPLASNIA----SVDLSIFSLHLAGASSLLGAINFMSTVINMRAETLTFDRLPLFVCSVFVTVILLLLSLPVLAGAITMLLTDRNLNT--FDPTGGGDPILYQHL"
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)
})
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