write_ortholog_fasta_files: Write fasta files from ortholog trees.

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

Given a folder containing ortholog trees, write out the fasta files that correspond to the sequences in the trees.

Usage

write_ortholog_fasta_files(
  path_to_ys = pkgconfig::get_config("baitfindR::path_to_ys"),
  all_fasta,
  tree_folder,
  outdir,
  minimal_taxa = 4,
  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 sequences.
outdir	Character vector of length one; the path to the folder where the fasta files should be written.
minimal_taxa	Numeric; minimal number of taxa required for output sequences to be written (regardless of ingroup/outgroup status).
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 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_ortholog_fasta_files.py

Value

One fasta file per tree will be written to outdir. If get_hash is TRUE, the 32-byte MD5 hash be computed for all .fa 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_ortholog_fasta_files(all_fasta = "some/folder/all.fasta", tree_folder = "some/folder/containing/tree/files", outdir = "some/folder", minimal_taxa = 5)

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