Nothing
test_that("A normal sequence in framed and translated properly", {
sequence = 'ctttacctgatttttggtgcatgagcaggtatagttggaacagccctaagtctcctaattcgagctgaacttgggcaacctggatcacttttaggagatgatcagatttataatgtaatcgtaaccgcccacgcttttgtaataatctttttcatggttataccaattataattggtggtttcggaaattgattagttcctttaataattggagcgccagatatagccttcccacgaataaataacataagtttctgacttcttccaccatcatttcttcttctcctcgcctctgctggagtagaagctggagcaggtactggttgaacagtttatcctccattagctagcaatctagcacatgctggaccatctgttgatttagctattttttctcttcacttagccggtgtttcatcaattttagcttcaattaattttatcacaaccattattaatataaaaccaccagctatttcccaatatcaaacaccattatttgtttgatctattcttgtaaccactattcttcttctcctctcacttccagttcttgcagcaggaattacaatattacttacagatcgtaaccttaatactacattctttgaccctgcaggtggaggagacccaatcctttatcaacattta'
sequence_framed = '---ctttacctgatttttggtgcatgagcaggtatagttggaacagccctaagtctcctaattcgagctgaacttgggcaacctggatcacttttaggagatgatcagatttataatgtaatcgtaaccgcccacgcttttgtaataatctttttcatggttataccaattataattggtggtttcggaaattgattagttcctttaataattggagcgccagatatagccttcccacgaataaataacataagtttctgacttcttccaccatcatttcttcttctcctcgcctctgctggagtagaagctggagcaggtactggttgaacagtttatcctccattagctagcaatctagcacatgctggaccatctgttgatttagctattttttctcttcacttagccggtgtttcatcaattttagcttcaattaattttatcacaaccattattaatataaaaccaccagctatttcccaatatcaaacaccattatttgtttgatctattcttgtaaccactattcttcttctcctctcacttccagttcttgcagcaggaattacaatattacttacagatcgtaaccttaatactacattctttgaccctgcaggtggaggagacccaatcctttatcaacattta'
seqname = 'test_seq1'
sequence_AAcensored = "-LYLIFGAWAG?VGTALSLLIRAELGQPGSLLGDDQIYNVIVTAHAFV?IFFMV?PI?IGGFGNWLVPL?IGAPD?AFPR?NN?SFWLLPPSFLLLLASAGVEAGAGTGWTVYPPLASNLAHAGPSVDLAIFSLHLAGVSSILASINFITTIIN??PPAISQYQTPLFVWSILVTTILLLLSLPVLAAGIT?LLTDRNLNTTFFDPAGGGDPILYQHL"
sequence_AA5 ="-LYLIFGAWAGMVGTALSLLIRAELGQPGSLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASAGVEAGAGTGWTVYPPLASNLAHAGPSVDLAIFSLHLAGVSSILASINFITTIINMKPPAISQYQTPLFVWSILVTTILLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHL"
dat = coi5p(sequence, name = seqname)
expect_equal(dat$raw, sequence)
expect_equal(dat$name, seqname)
dat = frame(dat)
expect_equal(dat$framed, sequence_framed)
dat = translate(dat)
expect_equal(dat$aaSeq, sequence_AAcensored)
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$stop_codons, FALSE)
#here is some additional sequences to test, it has a single outlier match prior to 4 deletes, then a string of matches
#need to change the frame logic so that this type of sequence is framed properly - back port the debar logic and see
#if performance is improved
seq_outlie = "TATGCTTTATTTTATTTTTGCTACCTGATCTGGAATGGTGGCTACAGGTTTAAGAGTTCTAATTCGAATTGAGCTAAGCGTTGCTACAGGCTGAATAGGAGACGATCAGCTTTACAACGTAATTGTTACGGCTCACGCTTTAATTATGTTATTTTTCTTTCTAATGCCTTTCCTTATGGGAGGATTTGGTAATACTCTTGTTCCTCTTATGATTGGAGCTCCAGACATGGCGTTCCCTCGAATGAACAACATGAGATTCTGAATGCTTCCCCCTTCTATGACACTTCTTCTAACATCTGCCCTAATTGAAAGAGGGGCAGGTACAGGATGGACTGTTTACCCTCCGCTATCAGGGATTGTATCCCATGCTGGTGGAAGGGTAGACTTGGCGATTTTTTCGTTACACCTTTCCGGTGCGTCTTCAATTTTAGGTACTGTAAATTTTCTTGCCACAGTGTTTAATATGCGAGGGCCTGGAATCACTTTCGAGCGAACCCCTCTATTTGTATGAGCTATGGTAGTTACAGTTGTTCTGTTACTTTTATCCCTTCCGGTATTTGCTGGTGGGATTACTATGCTACTTACAGATCGAAACTTCAATACTAGATTTTTCGATCCTGCTGGGGGTGGTGATCCTATTTTATTCCAGCACTTATTT"
dat = coi5p(seq_outlie)
dat = frame(dat)
processed_outlie = coi5p_pipe(seq_outlie)
#processed_outlie$indel_likely == FALSE
expect_equal(processed_outlie$indel_likely, FALSE)
#processed_outlie$stop_codons == FALSE
expect_equal(processed_outlie$stop_codons, FALSE)
#additional example - a sequence that was misframed on previous version, due to being slightly too long, but that has a good COI
#region
seq_left_add = "AATTTTATATTTTATTTTAGGTATATGATCAGGAATAATTGGTGCATCTATAAGTATTATTATTCGATTAGAATTAGGTAATCCTGGTTATTTAATTAATAATGATCAAATTTATAATTCTATTGTTACAGCCCATGCTTTCATTATAATTTTTTTTATAGTAATACCCATTATAATTGGAGGATTTGGTAATTGATTAATCCCATTAATACTTGGAGCTCCAGATATAGCATTTCCTCGAATAAATAATATAAGTTTTTGACTATTACCACCTTCACTATTATTATTATTAAATAGAAGATTAATTAATCAAGGTGTAGGAACCGGATGAACAGTTTATCCTCCTTTATCTTTAAATATTAATCATGAAGGTATATCAATTGATATAGCAATTTTTTCACTCCATCTTGCTGGTATATCATCAATTATAGGAGCAATTAATTTTATTACTACCATTATAAATATATTTCCATTAAAATTAAAATTTGAACAATTAACTTTATTTACATGATCAATTTTAATTACTACAATTTTATTATTAATTGCAGTACCTGTTTTAGCAGGAGCAATTACCATATTATTAACTGATCGAAATTTAAATACTTCATTTTTTGACCCATCCGGGGGAGGAGATCCAATTTTATATCAACATTTATTT"
dat = coi5p(seq_left_add)
dat = frame(dat)
#here is the long form code of the triple translate
d0 = translate(dat)
d0 = indel_check(d0)
d1 = translate(dat, frame_offset = 1)
d1 = indel_check(d1)
d2 = translate(dat, frame_offset = 2)
d2 = indel_check(d2)
scores = c(d0$aaScore,
d1$aaScore,
d2$aaScore)
best_frame = which.max(scores)
coi_objs = list(d0, d1, d2)
out = coi_objs[[best_frame]]
processed_left_add = coi5p_pipe(seq_left_add, triple_translate = TRUE)
#processed_left_add$stop_codons == FALSE
expect_equal(processed_left_add$stop_codons, FALSE)
})
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