Align all fasta files in a directory.

Given a directory containing unaligned fasta files, align all fasta files in the directory. If there are > 1000 sequences in the directory, use the mafft --auto algorithm. If less, use the --genafpair algorithm.

mafft_wrapper(path_to_ys = pkgconfig::get_config("baitfindR::path_to_ys"),
  fasta_folder, infile_ending = "fa", number_cores, seq_type = "dna",
  overwrite = FALSE, get_hash = TRUE,
  echo = pkgconfig::get_config("baitfindR::echo", fallback = FALSE), ...)

Arguments

path_to_ys	Character vector of length one; the path to the folder containing Y&S python scripts, e.g., "/Users/me/apps/phylogenomic_dataset_construction/"
fasta_folder	Character vector of length one; the path to the folder containing the fasta files to be aligned.
infile_ending	Character vector of length one; only files with this ending will be included.
number_cores	Numeric; number of threads to use for and mafft.
seq_type	Character vector of length one indicating type of sequences. Should either be "dna" for DNA or "aa" for proteins.
overwrite	Logical; should previous output of this command be erased so new output can be written? Once erased it cannot be restored, so use with caution!
get_hash	Logical; should the 32-byte MD5 hash be computed for all aligned fasta files concatenated together? Used for by drake_plan for tracking during workflows. If TRUE, this function will return the hash.
echo	Logical; should the standard output and error be printed to the screen?
...	Other arguments. Not used by this function, but meant to be used by drake_plan for tracking during workflows.

Value

Aligned fasta files will be written to fasta_folder with the file ending .aln. If get_hash is TRUE, the 32-byte MD5 hash be computed for all .aln files concatenated together will be returned.

Details

Wrapper for Yang and Smith (2014) mafft_wrapper.py

References

Yang, Y. and S.A. Smith. 2014. Orthology inference in non-model organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution 31:3081-3092. https://bitbucket.org/yangya/phylogenomic_dataset_construction/overview

Examples

# NOT RUN {
mafft_wrapper(fasta_folder = "some/folder/with/fasta/files", number_cores = 2, seq_type = "dna")
# }