test_that("use", {
expect_silent(
create_beast2_input_data_sequences(
get_fasta_filename(),
beauti_options = create_beauti_options(nucleotides_uppercase = FALSE)
)
)
expect_silent(
create_beast2_input_data_sequences(
get_fasta_filename(),
beauti_options = create_beauti_options(nucleotides_uppercase = TRUE)
)
)
})
test_that("v2.4", {
created <- create_beast2_input_data_sequences(
input_fasta_filename = get_fasta_filename(),
beauti_options = create_beauti_options_v2_4()
)
expected <- c(
" <sequence id=\"seq_t1\" taxon=\"t1\" totalcount=\"4\" value=\"acttgttgcgactgcgcctg\"/>", # nolint long line indeed
" <sequence id=\"seq_t2\" taxon=\"t2\" totalcount=\"4\" value=\"acttattgcgactgaggccg\"/>", # nolint long line indeed
" <sequence id=\"seq_t3\" taxon=\"t3\" totalcount=\"4\" value=\"acttaatgcgaatgagcccg\"/>", # nolint long line indeed
" <sequence id=\"seq_t4\" taxon=\"t4\" totalcount=\"4\" value=\"aacgacccgcgatcggggat\"/>", # nolint long line indeed
" <sequence id=\"seq_t5\" taxon=\"t5\" totalcount=\"4\" value=\"acttgttgcgactgagcctg\"/>" # nolint long line indeed
)
expect_equal(expected, created)
})
test_that("v2.6", {
created <- create_beast2_input_data_sequences(
input_fasta_filename = get_fasta_filename(),
beauti_options = create_beauti_options_v2_6()
)
expected <- c(
" <sequence id=\"seq_t1\" spec=\"Sequence\" taxon=\"t1\" totalcount=\"4\" value=\"acttgttgcgactgcgcctg\"/>", # nolint indeed a long line
" ",
" <sequence id=\"seq_t2\" spec=\"Sequence\" taxon=\"t2\" totalcount=\"4\" value=\"acttattgcgactgaggccg\"/>", # nolint indeed a long line
" ",
" <sequence id=\"seq_t3\" spec=\"Sequence\" taxon=\"t3\" totalcount=\"4\" value=\"acttaatgcgaatgagcccg\"/>", # nolint indeed a long line
" ",
" <sequence id=\"seq_t4\" spec=\"Sequence\" taxon=\"t4\" totalcount=\"4\" value=\"aacgacccgcgatcggggat\"/>", # nolint indeed a long line
" ",
" <sequence id=\"seq_t5\" spec=\"Sequence\" taxon=\"t5\" totalcount=\"4\" value=\"acttgttgcgactgagcctg\"/>" # nolint indeed a long line
)
expect_equal(expected, created)
})
test_that("abuse", {
expect_error(
create_beast2_input_data_sequences("nonse.nse")
)
})
test_that("sort order", {
fasta_filename_1 <- get_beautier_path("anthus_nd2.fas")
lines <- create_beast2_input_data_sequences(fasta_filename_1)
expect_true(substr(lines[11], 35, 46) != "seq_bas3_nd2")
expect_true(substr(lines[11], 35, 47) == "seq_FALK1_nd2")
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.