write_fasta_files_from_trees: Write fasta files from trees.

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

Given a folder containing phylogenetic trees and a single concatenated fasta file including all the sequences used to build the trees, output one fasta file per tree with the sequences in that tree. This function will overwrite any output files with the same name in outdir.

Usage

write_fasta_files_from_trees(
  path_to_ys = pkgconfig::get_config("baitfindR::path_to_ys"),
  all_fasta,
  tree_folder,
  tree_file_ending,
  outdir,
  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/"
all_fasta	Character vector of length one; the path to the fasta file including all the sequences that were originally used to build the trees.
tree_folder	Character vector of length one; the path to the folder containing the trees to be used for extracting fasta sequences.
tree_file_ending	Character vector of length one; only tree files with this file ending will be used.
outdir	Character vector of length one; the path to the folder where the fasta files should be written.
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 output 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.

Details

Wrapper for Yang and Smith (2014) write_fasta_files_from_trees.py

Value

One fasta file per tree file ending in tree_file_ending in tree_folder will be written to outdir. If get_hash is TRUE, the 32-byte MD5 hash be computed for all output fasta files concatenated together will be returned.

Author(s)

Joel H Nitta, [e-mail]

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: write_fasta_files_from_trees(all_fasta = "some/folder/all.fasta", tree_file_ending = ".subtree", tree_folder = "some/folder/containing/tree/files", outdir = "some/folder")

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