aliscore, alicut

R/phylo.R

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+#' @title wrapper to run Aliscore
+#'
+#' @details aliscore will produce several files under the directory containg input files
+#'
+#' @param args character. options for `Aliscore.0x.y.pl`
+#' @param ... other parameters passed on to [system2()]
+#'
+#' @return result of [system2()]
+#' @export
+#'
+#' @examples
+#' \donotrun {
+#'     aliscore('-i data-raw/aliscore/test.fasta')
+#' }
+aliscore <- function(args, ...) {
+	args %<>% c('-I', pkg_file('lib'), pkg_file('exec/Aliscore.02.2.pl'), .)
+	system2('perl', args, ...);
+}
+
+
+#' @title wrapper to run Alicut
+#'
+#' @param dir string. the directory your input files lie. working directory will
+#'   be temporarily set to it
+#' @param ... other parameters passed on to [system2()], including `args` and so
+#'   on.
+#'
+#' @return result of [system2()]
+#' @export
+#'
+#' @examples
+#' \donotrun {
+#'     aliscore('-i data-raw/aliscore/test.fasta');
+#'     alicut('data-raw/aliscore', args = '-s')
+#' }
+alicut <- function(dir, ...) {
+	old_wd <- getwd();
+	on.exit(setwd(old_wd));
+
+	setwd(dir);
+	system2(pkg_file('exec/ALICUT_V2.31.pl'), ...);
+}
+
+
+
+

tests/testthat.R

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+library(testthat)
+library(biozhuoer)
+
+test_check("biozhuoer")

tests/testthat/test-phylo.R

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+context("Testing phylo")
+
+setwd('../..');
+
+dir('data-raw/aliscore/', full.names = T) %>% file.remove()
+file.copy('data-raw/aligned-multiline.fasta', 'data-raw/aliscore/test.fasta');
+
+test_that("Testing aliscore", {
+    expect_identical(aliscore('-i data-raw/aliscore/test.fasta', F, F), 0L);
+});
+
+test_that("Testing alicut", {
+    expect_identical(alicut('data-raw/aliscore', '-s'), 0L);
+});
+