Write out a list of fasta files to a directory

Optionally assign names to the files if `fasta_list` isn't already named or if you want to over-write the original names.

write_fasta_files(fasta_list, out_dir, fasta_names = NULL, ext = NULL,
  get_hash = TRUE, ...)

Arguments

fasta_list	List of DNA sequences to write out. Each item in list must of class DNAbin.
out_dir	Path to directory to write out DNA sequences.
fasta_names	Optional character vector of file names to use when writing out DNA sequences.
ext	Optional character vector of length one; file extension to append to DNA sequences (e.g., "fasta").
get_hash	Logical; should the MD5 hash of `fasta_list` be returned?
...	Additional other arguments. Not used by this function, but meant to be used by drake_plan for tracking during workflows.

Value

None (invisible ‘NULL’) or character vector if `hash` is `TRUE`. Externally, fasta files will be written to `out_dir`.

Examples

# Load some example DNA sequences.
library(ape)
data(woodmouse)

# Make a temporary working directory to write out files.
temp_dir <- fs::dir_create(fs::path(tempdir(), "baitfindR_example"))

# Make list of DNA samples.
dna_list <- list(a = woodmouse, b = woodmouse)

# Write out list:
# names as-is
write_fasta_files(dna_list, temp_dir)
#> [1] "5a3f4d3219877f7afa647fe25e8ae0a8"
list.files(temp_dir)
#> [1] "a" "b"

# add extension
write_fasta_files(dna_list, temp_dir, ext = "fasta")
#> [1] "5a3f4d3219877f7afa647fe25e8ae0a8"
list.files(temp_dir)
#> [1] "a"       "a.fasta" "b"       "b.fasta"

# new names and extension
write_fasta_files(
  dna_list,
  temp_dir,
  fasta_names = c("ho", "ge"),
  ext = "fasta")
#> [1] "d67912fe5606116cac2937adc96000eb"
list.files(temp_dir)
#> [1] "a"        "a.fasta"  "b"        "b.fasta"  "ge.fasta" "ho.fasta"

# Cleanup
fs::file_delete(temp_dir)