context("Testing seqaln")

test_that("seqaln works", {

  ## seqaln with one sequence. should remove gaps
  seqs <- c("X", "-", "-", "A", "C", "A", "G", "K", "-")
  aln <- seqaln(seqs)
  expected <- c("X", "A", "C", "A", "G", "K")
  expect_identical(c(aln$ali), expected)

  ## align two sequences
  seqs <- seqbind(seqs,
                c("C", "A", "G", "G", "A", "G", "K"))
  aln <- seqaln(seqs)
  expected <- seqbind(c("-", "X", "A", "C", "A", "G", "K"),
                      c("C", "A", "G", "G", "A", "G", "K"))
  expect_identical(aln$ali, expected$ali)

  ## add a sequence to the (profile) alignment
  seq <- c("G", "A", "G", "K", "-")
  aln <- seqaln(seq, profile=aln)
  rownames(aln$ali) <- paste0("seq", 1:3)
  expected <- seqbind(c("-", "X", "A", "C", "A", "G", "K", "-"),
                      c("C", "A", "G", "G", "A", "G", "K", "-"),
                      c("-", "-", "-", "G", "A", "G", "K", "-"))
  expect_identical(aln$ali, expected$ali)



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bio3d documentation built on July 31, 2017, 9:01 a.m.