Nothing
library(testthat)
library(AnaCoDa)
context("Sequence Summary")
test_that("general sequence summary functions", {
expect_equal(testSequenceSummary(), 0)
})
#Used to test AAToCodonRange, but that is now returned by
#reference and cannot deal with that in R. Since this will
#change with codonTable being completed, the tests have been
#ommitted for the time being.
#this function will be moved to CodonTable when it is finished.
test_that("AA To Codon", {
expect_equal(AAToCodon("A", FALSE), c("GCA", "GCC", "GCG", "GCT"))
expect_equal(AAToCodon("C", FALSE), c("TGC", "TGT"))
expect_equal(AAToCodon("D", FALSE), c("GAC", "GAT"))
expect_equal(AAToCodon("E", FALSE), c("GAA", "GAG"))
expect_equal(AAToCodon("F", FALSE), c("TTC", "TTT"))
expect_equal(AAToCodon("G", FALSE), c("GGA", "GGC", "GGG", "GGT"))
expect_equal(AAToCodon("H", FALSE), c("CAC", "CAT"))
expect_equal(AAToCodon("I", FALSE), c("ATA", "ATC", "ATT"))
expect_equal(AAToCodon("K", FALSE), c("AAA", "AAG"))
expect_equal(AAToCodon("L", FALSE), c("CTA", "CTC", "CTG", "CTT", "TTA", "TTG"))
expect_equal(AAToCodon("M", FALSE), c("ATG"))
expect_equal(AAToCodon("N", FALSE), c("AAC", "AAT"))
expect_equal(AAToCodon("P", FALSE), c("CCA", "CCC", "CCG", "CCT"))
expect_equal(AAToCodon("Q", FALSE), c("CAA", "CAG"))
expect_equal(AAToCodon("R", FALSE), c("AGA", "AGG", "CGA", "CGC", "CGG", "CGT"))
expect_equal(AAToCodon("S", FALSE), c("TCA", "TCC", "TCG", "TCT"))
expect_equal(AAToCodon("T", FALSE), c("ACA", "ACC", "ACG", "ACT"))
expect_equal(AAToCodon("V", FALSE), c("GTA", "GTC", "GTG", "GTT"))
expect_equal(AAToCodon("W", FALSE), c("TGG"))
expect_equal(AAToCodon("Y", FALSE), c("TAC", "TAT"))
expect_equal(AAToCodon("Z", FALSE), c("AGC", "AGT"))
expect_equal(AAToCodon("X", FALSE), c("TAA", "TAG", "TGA"))
expect_equal(AAToCodon("A", TRUE), c("GCA", "GCC", "GCG"))
expect_equal(AAToCodon("C", TRUE), c("TGC"))
expect_equal(AAToCodon("D", TRUE), c("GAC"))
expect_equal(AAToCodon("E", TRUE), c("GAA"))
expect_equal(AAToCodon("F", TRUE), c("TTC"))
expect_equal(AAToCodon("G", TRUE), c("GGA", "GGC", "GGG"))
expect_equal(AAToCodon("H", TRUE), c("CAC"))
expect_equal(AAToCodon("I", TRUE), c("ATA", "ATC"))
expect_equal(AAToCodon("K", TRUE), c("AAA"))
expect_equal(AAToCodon("L", TRUE), c("CTA", "CTC", "CTG", "CTT", "TTA"))
expect_equal(AAToCodon("M", TRUE), character(0))
expect_equal(AAToCodon("N", TRUE), c("AAC"))
expect_equal(AAToCodon("P", TRUE), c("CCA", "CCC", "CCG"))
expect_equal(AAToCodon("Q", TRUE), c("CAA"))
expect_equal(AAToCodon("R", TRUE), c("AGA", "AGG", "CGA", "CGC", "CGG"))
expect_equal(AAToCodon("S", TRUE), c("TCA", "TCC", "TCG"))
expect_equal(AAToCodon("T", TRUE), c("ACA", "ACC", "ACG"))
expect_equal(AAToCodon("V", TRUE), c("GTA", "GTC", "GTG"))
expect_equal(AAToCodon("W", TRUE), character(0))
expect_equal(AAToCodon("Y", TRUE), c("TAC"))
expect_equal(AAToCodon("Z", TRUE), c("AGC"))
expect_equal(AAToCodon("X", TRUE), character(0))
})
test_that("Amino Acid Vector", {
expect_equal(aminoAcids(), c(
"A",
"C",
"D",
"E",
"F",
"G",
"H",
"I",
"K",
"L",
"M",
"N",
"P",
"Q",
"R",
"S",
"T",
"V",
"W",
"Y",
"Z",
"X"))
})
test_that("Codon Vector", {
expect_equal(codons(), c(
"GCA",
"GCC",
"GCG",
"GCT",
"TGC",
"TGT",
"GAC",
"GAT",
"GAA",
"GAG",
"TTC",
"TTT",
"GGA",
"GGC",
"GGG",
"GGT",
"CAC",
"CAT",
"ATA",
"ATC",
"ATT",
"AAA",
"AAG",
"CTA",
"CTC",
"CTG",
"CTT",
"TTA",
"TTG",
"ATG",
"AAC",
"AAT",
"CCA",
"CCC",
"CCG",
"CCT",
"CAA",
"CAG",
"AGA",
"AGG",
"CGA",
"CGC",
"CGG",
"CGT",
"TCA",
"TCC",
"TCG",
"TCT",
"ACA",
"ACC",
"ACG",
"ACT",
"GTA",
"GTC",
"GTG",
"GTT",
"TGG",
"TAC",
"TAT",
"AGC",
"AGT",
"TAA",
"TAG",
"TGA"
))
})
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