Description Usage Arguments Examples
Run the muleiple alignment program mafft.
1 |
arglist |
Arguments as character vector passed to mafft |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | library(outsider)
# import
mafft <- module_import('mafft', repo = 'dombennett/om..mafft')
# get help
mafft('--help')
# download
wd <- file.path(tempdir(), 'mafft_example')
if (!dir.exists(wd)) {
dir.create(wd)
}
# example DNA
seq_file <- file.path(wd, 'example_seq.fasta')
url <- 'https://raw.githubusercontent.com/DomBennett/om..pasta/master/example_seq.fasta'
download.file(url = url, destfile = seq_file)
# align
al_file <- file.path(wd, 'alignment.fasta')
mafft(arglist = c('--auto', seq_file, '>', al_file))
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