Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup--------------------------------------------------------------------
library(pureseqtmr)
library(testthat)
library(knitr)
## -----------------------------------------------------------------------------
if (is_pureseqtm_installed()) {
get_example_filenames()
}
## -----------------------------------------------------------------------------
if (is_pureseqtm_installed()) {
fasta_filename <- get_example_filename("1bhaA.fasta")
head(readLines(fasta_filename))
}
## -----------------------------------------------------------------------------
if (is_pureseqtm_installed()) {
topology <- predict_topology(fasta_filename)
kable(topology)
}
## ----fig.width=7--------------------------------------------------------------
if (is_pureseqtm_installed()) {
plot_topology(topology)
}
## -----------------------------------------------------------------------------
fasta_filename <- system.file(
"extdata",
"UP000464024.fasta",
package = "pureseqtmr"
)
expect_true(file.exists(fasta_filename))
## -----------------------------------------------------------------------------
head(readLines(fasta_filename))
## -----------------------------------------------------------------------------
if (is_pureseqtm_installed()) {
topology <- predict_topology(fasta_filename)
}
## -----------------------------------------------------------------------------
if (is_pureseqtm_installed()) {
topology$name <- stringr::str_match(
string = topology$name,
pattern = "..\\|.*\\|(.*)_SARS2"
)[, 2]
}
## ----fig.width=7--------------------------------------------------------------
if (is_pureseqtm_installed()) {
plot_topology(topology)
}
## -----------------------------------------------------------------------------
if (is_pureseqtm_installed()) {
kable(tally_tmhs(topology))
}
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