Nothing
context("Testing seqaln")
test_that("seqaln works", {
skip_on_cran()
skip_on_travis()
## seqaln with one sequence. should remove gaps
seqs <- c("X", "-", "-", "A", "C", "A", "G", "K", "-")
suppressWarnings( 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)
## test 'msa' option
if( requireNamespace("msa", quietly=TRUE) ) {
capture.output( seqs <- get.seq(c("4q21_A", "1ftn_A"), outfile=tempfile()) )
aln <- seqaln(seqs, outfile=tempfile())
aln2 <- seqaln(seqs, outfile=tempfile(), exefile="msa")
aln$call <- NULL; aln2$call <- NULL
expect_identical(aln, aln2)
}
})
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