# -*- tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
# vi: set ts=2 noet:
#' Run phyml
#' @export
phyml <- function(
phylip,
run_id = NULL,
run_script_fname = NULL,
data_type = 'aa',
model = "LG",
search = "NNI",
ncores=18,
max_mem=10000,
output_fmt="phylip",
seqtype="protein"
){
input_base <- tempfile()
if(is.character(phylip)){
if(
!stringr::str_detect(phylip, ".phylip$") &&
!stringr::str_detect(phylip, ".phy") &&
!stringr::str_detect(phylip, ".ph")){
cat("WARNING: phylip '", phylip, "', does not end in '.phy', '.ph', or '.phylip'\n")
}
phylip_fname <- phylip
} else {
stop("Currently I don't know how to convert an R file into a .phylip MSA\n")
}
if(is.null(run_id)){
run_id = stringr::str_replace(phylip_fname, ".phylip$", "")
}
cmd <- paste0(
"phyml ",
"--input ", shQuote(phylip_fname), " ",
"--datatype ", data_type, " ",
"--model ", model, " ",
"--search ", search, " ",
"--run_id ", shQuote(run_id), " ",
"--quiet ",
"--no_memory_check ")
if(!is.null(run_script_fname)){
cat(
"#Run PhyML\n",
cmd, "\n\n", sep="", file=run_script_fname, append=T)
}
cat(cmd, "\n")
system(cmd)
}
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