write_fasta_files: Write out a list of fasta files to a directory

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

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

Usage

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)
list.files(temp_dir)

# add extension
write_fasta_files(dna_list, temp_dir, ext = "fasta")
list.files(temp_dir)

# new names and extension
write_fasta_files(
  dna_list,
  temp_dir,
  fasta_names = c("ho", "ge"),
  ext = "fasta")
list.files(temp_dir)

# Cleanup
fs::file_delete(temp_dir)

joelnitta/baitfindR documentation built on May 7, 2020, 6:21 p.m.