tests/testthat/test-multipleSeqAlign.R

In quick2063706271/Cov2Comparator: Analyzing SARS covid-2 genome across different geographic regions

library(Cov2Comparator)

test_that("test simple multiple sequence alignment", {
  suppressPackageStartupMessages(library(Biostrings))
  set1 <- Biostrings::DNAStringSet("ATCGATCG")
  set2 <- Biostrings::DNAStringSet("ATTTTTTT")
  set3 <- Biostrings::DNAStringSet("ATCGATTT")
  setTotal <- union(set1, set2)
  setTotal <- union(setTotal, set3)
  align <- Biostrings::unmasked(multipleSeqAlign(Biostrings::DNAStringSet(setTotal)))
  expect_length(align, 3)
})

test_that("test getSequenceByRegion using Muscle", {
  suppressPackageStartupMessages(library(Biostrings))
  set1 <- Biostrings::DNAStringSet("ATCGATCG")
  set2 <- Biostrings::DNAStringSet("ATTTTTTT")
  set3 <- Biostrings::DNAStringSet("ATCGATTT")
  setTotal <- union(set1, set2)
  setTotal <- union(setTotal, set3)
  align <- Biostrings::unmasked(multipleSeqAlign(Biostrings::DNAStringSet(setTotal), algorithm = "Muscle"))
  expect_length(align, 3)
})

test_that("test getSequenceByRegion using wrong sequences", {
  suppressPackageStartupMessages(library(Biostrings))
  setTotal <- "AASSAASS"
  expect_error(multipleSeqAlign(setTotal))
})