context("translation")
test_that("translate correctly translates codons",{
# I
expect_that(translate(c("A","T","T"), FALSE), equals("I"))
expect_that(translate(c("A","T","C"), FALSE), equals("I"))
expect_that(translate(c("A","T","A"), FALSE), equals("I"))
# L
expect_that(translate(c("C","T","T"), FALSE), equals("L"))
expect_that(translate(c("C","T","C"), FALSE), equals("L"))
expect_that(translate(c("C","T","A"), FALSE), equals("L"))
expect_that(translate(c("C","T","G"), FALSE), equals("L"))
expect_that(translate(c("T","T","A"), FALSE), equals("L"))
expect_that(translate(c("T","T","G"), FALSE), equals("L"))
# V
expect_that(translate(c("G","T","T"), FALSE), equals("V"))
expect_that(translate(c("G","T","C"), FALSE), equals("V"))
expect_that(translate(c("G","T","A"), FALSE), equals("V"))
expect_that(translate(c("G","T","G"), FALSE), equals("V"))
# F
expect_that(translate(c("T","T","T"), FALSE), equals("F"))
expect_that(translate(c("T","T","C"), FALSE), equals("F"))
# M
expect_that(translate(c("A","T","G"), FALSE), equals("M"))
# C
expect_that(translate(c("T","G","T"), FALSE), equals("C"))
expect_that(translate(c("T","G","C"), FALSE), equals("C"))
# A
expect_that(translate(c("G","C","T"), FALSE), equals("A"))
expect_that(translate(c("G","C","C"), FALSE), equals("A"))
expect_that(translate(c("G","C","A"), FALSE), equals("A"))
expect_that(translate(c("G","C","G"), FALSE), equals("A"))
# G
expect_that(translate(c("G","G","T"), FALSE), equals("G"))
expect_that(translate(c("G","G","C"), FALSE), equals("G"))
expect_that(translate(c("G","G","A"), FALSE), equals("G"))
expect_that(translate(c("G","G","G"), FALSE), equals("G"))
# P
expect_that(translate(c("C","C","T"), FALSE), equals("P"))
expect_that(translate(c("C","C","C"), FALSE), equals("P"))
expect_that(translate(c("C","C","A"), FALSE), equals("P"))
expect_that(translate(c("C","C","G"), FALSE), equals("P"))
# T
expect_that(translate(c("A","C","T"), FALSE), equals("T"))
expect_that(translate(c("A","C","C"), FALSE), equals("T"))
expect_that(translate(c("A","C","A"), FALSE), equals("T"))
expect_that(translate(c("A","C","G"), FALSE), equals("T"))
# S
expect_that(translate(c("T","C","T"), FALSE), equals("S"))
expect_that(translate(c("T","C","C"), FALSE), equals("S"))
expect_that(translate(c("T","C","A"), FALSE), equals("S"))
expect_that(translate(c("T","C","G"), FALSE), equals("S"))
expect_that(translate(c("A","G","T"), FALSE), equals("S"))
expect_that(translate(c("A","G","C"), FALSE), equals("S"))
# Y
expect_that(translate(c("T","A","T"), FALSE), equals("Y"))
expect_that(translate(c("T","A","C"), FALSE), equals("Y"))
# W
expect_that(translate(c("T","G","G"), FALSE), equals("W"))
# Q
expect_that(translate(c("C","A","A"), FALSE), equals("Q"))
expect_that(translate(c("C","A","G"), FALSE), equals("Q"))
# N
expect_that(translate(c("A","A","T"), FALSE), equals("N"))
expect_that(translate(c("A","A","C"), FALSE), equals("N"))
# H
expect_that(translate(c("C","A","T"), FALSE), equals("H"))
expect_that(translate(c("C","A","C"), FALSE), equals("H"))
# E
expect_that(translate(c("G","A","A"), FALSE), equals("E"))
expect_that(translate(c("G","A","G"), FALSE), equals("E"))
# D
expect_that(translate(c("G","A","T"), FALSE), equals("D"))
expect_that(translate(c("G","A","C"), FALSE), equals("D"))
# K
expect_that(translate(c("A","A","A"), FALSE), equals("K"))
expect_that(translate(c("A","A","G"), FALSE), equals("K"))
# R
expect_that(translate(c("C","G","T"), FALSE), equals("R"))
expect_that(translate(c("C","G","C"), FALSE), equals("R"))
expect_that(translate(c("C","G","A"), FALSE), equals("R"))
expect_that(translate(c("C","G","G"), FALSE), equals("R"))
expect_that(translate(c("A","G","A"), FALSE), equals("R"))
expect_that(translate(c("A","G","G"), FALSE), equals("R"))
expect_that({
set.seed(10)
nt_seq <- generate_sequence(3, FALSE, FALSE)
p_seq <- translate(nt_seq, FALSE)
},
equals(c("A","V","P"))
)
}
)
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