tests/testthat/test_codonAdaptionIndex.R

In ftrCOOL: Feature Extraction from Biological Sequences

context("Just testing codonAdaptionIndex functionality")

test_that("Check codonAdaptionIndex works properly",{

  CodonAI<-codonAdaptionIndex(seqs=c("ATACGAATCATA","ATGGTCCTCATGGTGGTG"))

  codonList<-list("A"=c("GCT","GCC","GCA","GCG"),"R"=c("AGA","AGG","CGT","CGC","CGA","CGG"),
                    "N"=c("AAT","AAC"),"D"=c("GAT","GAC"),"C"=c("TGT","TGC"),"Q"=c("CAA","CAG"),
                    "E"=c("GAA","GAG"),"G"=c("GGT","GGC","GGA","GGG"),"H"=c("CAT","CAC"),
                    "I"=c("ATT","ATC","ATA"),"L"=c("TTA","TTG","CTT","CTC","CTA","CTG"),"K"=c("AAA","AAG"),
                    "M"=c("ATG"),"F"=c("TTT","TTC"),"P"=c("CCT","CCC","CCA","CCG"),
                    "S"=c("AGT","AGC","TCT","TCC","TCA","TCG"),"T"=c("ACT","ACC","ACA","ACG"),"W"=c("TGG"),
                    "Y"=c("TAT","TAC"),"V"=c("GTT","GTC","GTA","GTG"),"STOPcod"=c("TAA","TAG","TGA"))
# I=ATA R=CGA I=ATC I=ATA
 # M=ATG V=GTC L=CTC M=ATG V=GTG v=GTG
  codonVector<-unlist(codonList)
  numCodon<-length(codonVector)
  expected_matrix<-matrix(0,ncol = numCodon,nrow = 2)
  colnames(expected_matrix)<-codonVector
  expected_matrix[1,c("ATA","CGA","ATC")]<-c(2/2,1,1/2)
  expected_matrix[2,c("ATG","GTC","CTC","GTG")]<-c(2/2,1/2,1,2/2)
  expectedCodon<-vector()
  expectedCodon[1]<-prod(c(2/2,1,1/2))^(1/12)
  expectedCodon[2]<-prod(c(2/2,1/2,1,2/2))^(1/18)
  names(expectedCodon)<-NULL
  names(CodonAI)<-NULL
  expect_equal(CodonAI,expectedCodon)

  CodonAI2<-codonAdaptionIndex(seqs=c("ATACGAATCATATC","ATGGTCCTCATGGTGGTGTC"))
  names(CodonAI2)<-NULL
  expectedCodon2<-vector()
  expectedCodon2[1]<-prod(c(2/2,1,1/2))^(1/14)
  expectedCodon2[2]<-prod(c(2/2,1/2,1,2/2))^(1/20)
  expect_equal(CodonAI2,expectedCodon2)

})