Nothing
test_that("The reading frame of sequences is reported properly", {
long_sequence = 'aaccgctgattattttcaaccaaccacaaagatatcggcaaactttatattttatttttggagcttgagctggaatagttggaacatctttaagaattttaattcgagctgaattaggacatcctggagcattaattggagatgatcaaatttataatgtaattgtaactgcacatgcttttattataattttttttatggttatacctattataattggtggatttggaaattgattagtgcctttaatattaggtgctcctgatatagcattcccacgaataaataatataagattttgactactacctcctgctctttctttactattagtaagtagaatagttgaaaatggagctggaacaggatgaactgtttatccacctttatccgctggaattgctcatggtggagcttcagttgatttagctattttttctctacatttagcagggatttcttcaattttaggagctctaaattttattacaactgtaattaatatacgatcaacaggaatttcattagatcgtatacctttatttgtttgatcagtagttattactgctttattattgttattatcacttccagtactagcaggagctattactatattattaacagatcgaaatttaaatacatcattttttgacccagcgggaggaggagatcctattttatatcaacatttattatttattta'
long_sequence_framed = 'actttatattttatttttggagcttgagctggaatagttggaacatctttaagaattttaattcgagctgaattaggacatcctggagcattaattggagatgatcaaatttataatgtaattgtaactgcacatgcttttattataattttttttatggttatacctattataattggtggatttggaaattgattagtgcctttaatattaggtgctcctgatatagcattcccacgaataaataatataagattttgactactacctcctgctctttctttactattagtaagtagaatagttgaaaatggagctggaacaggatgaactgtttatccacctttatccgctggaattgctcatggtggagcttcagttgatttagctattttttctctacatttagcagggatttcttcaattttaggagctctaaattttattacaactgtaattaatatacgatcaacaggaatttcattagatcgtatacctttatttgtttgatcagtagttattactgctttattattgttattatcacttccagtactagcaggagctattactatattattaacagatcgaaatttaaatacatcattttttgacccagcgggaggaggagatcctattttatatcaacattta'
#expected:
#41 leading bp trimmed
x_long = 42
y_long = 1
long_desc = paste0("Base pair ", x_long, " of the raw sequence is base pair ", y_long, " of the COI-5P region.")
long_dat = coi5p(long_sequence, name = 'long_frame_report')
long_dat = frame(long_dat)
long_dat$data$raw_int_trim
long_dat$data$raw_start
long_dat$data$folmer_start
long_dat$align_report
long_dat$was_trimmed
# long_desc == long_dat$align_report
expect_equal(long_desc, long_dat$align_report)
short_sequence = 'tatgctagggaccgcagttagtgtgattattcgtgctgagttaggacagccaggatcacttattgggaacgatcaaatttacaatacaattgtgactgctcatgcctttattataattttcttcatggtgatacctatcataatcggaggattcggtaattgactggtaccggtaatactaggagcaccagatatagctttccctcgtatgaacaacataagattttgattactccctccttccttaacccttcttataatcgggatactaacagaaagaggggcaggaacaggatgaactgtataccctcctctctcaagaaatatccctcactcaggagctagagtagacctaacaattttttcactacatttagctggagccaggtcacttcttggggctattaatttcatcacaacaattattaatatacgagcagctagaatatctcttgatcgaattcctttatttg'
short_sequence_framed = '--------------------------------tatgctagggaccgcagttagtgtgattattcgtgctgagttaggacagccaggatcacttattgggaacgatcaaatttacaatacaattgtgactgctcatgcctttattataattttcttcatggtgatacctatcataatcggaggattcggtaattgactggtaccggtaatactaggagcaccagatatagctttccctcgtatgaacaacataagattttgattactccctccttccttaacccttcttataatcgggatactaacagaaagaggggcaggaacaggatgaactgtataccctcctctctcaagaaatatccctcactcaggagctagagtagacctaacaattttttcactacatttagctggagccaggtcacttcttggggctattaatttcatcacaacaattattaatatacgagcagctagaatatctcttgatcgaattcctttattt'
x_short = 1
y_short = 33
short_desc = paste0("Base pair ", x_short, " of the raw sequence is base pair ", y_short, " of the COI-5P region.")
short_dat = coi5p(short_sequence, name = 'short_frame_report')
short_dat = frame(short_dat)
short_dat$data$raw_start
short_dat$data$folmer_start
# short_desc == short_dat$align_report
expect_equal(short_desc, short_dat$align_report)
normal_sequence = 'ctttacctgatttttggtgcatgagcaggtatagttggaacagccctaagtctcctaattcgagctgaacttgggcaacctggatcacttttaggagatgatcagatttataatgtaatcgtaaccgcccacgcttttgtaataatctttttcatggttataccaattataattggtggtttcggaaattgattagttcctttaataattggagcgccagatatagccttcccacgaataaataacataagtttctgacttcttccaccatcatttcttcttctcctcgcctctgctggagtagaagctggagcaggtactggttgaacagtttatcctccattagctagcaatctagcacatgctggaccatctgttgatttagctattttttctcttcacttagccggtgtttcatcaattttagcttcaattaattttatcacaaccattattaatataaaaccaccagctatttcccaatatcaaacaccattatttgtttgatctattcttgtaaccactattcttcttctcctctcacttccagttcttgcagcaggaattacaatattacttacagatcgtaaccttaatactacattctttgaccctgcaggtggaggagacccaatcctttatcaacattta'
normal_sequence_framed = '---ctttacctgatttttggtgcatgagcaggtatagttggaacagccctaagtctcctaattcgagctgaacttgggcaacctggatcacttttaggagatgatcagatttataatgtaatcgtaaccgcccacgcttttgtaataatctttttcatggttataccaattataattggtggtttcggaaattgattagttcctttaataattggagcgccagatatagccttcccacgaataaataacataagtttctgacttcttccaccatcatttcttcttctcctcgcctctgctggagtagaagctggagcaggtactggttgaacagtttatcctccattagctagcaatctagcacatgctggaccatctgttgatttagctattttttctcttcacttagccggtgtttcatcaattttagcttcaattaattttatcacaaccattattaatataaaaccaccagctatttcccaatatcaaacaccattatttgtttgatctattcttgtaaccactattcttcttctcctctcacttccagttcttgcagcaggaattacaatattacttacagatcgtaaccttaatactacattctttgaccctgcaggtggaggagacccaatcctttatcaacattta'
x_norm = 1
y_norm = 4
normal_desc = paste0("Base pair ", x_norm, " of the raw sequence is base pair ", y_norm, " of the COI-5P region.")
normal_dat = coi5p(normal_sequence, name = 'normal_frame_report')
normal_dat = frame(normal_dat)
# normal_desc == normal_dat$align_report
expect_equal(normal_desc, normal_dat$align_report)
# COI is defined relative to the mouse mitochondrial genome as the
# 648 bp region that starts at position 58 and stops at position 705
# The PHMM only spans the first 657bp of the sequence
})
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