check_taxon_ids: Check Genbank taxon IDs

In grunwaldlab/oomycetedbtools: Tools for managing the OomyceteDB website and database

Check Genbank taxon IDs

Description

Checks that Genbank taxon IDs are valid.

Usage

check_taxon_ids(
  database_path = NULL,
  release_path = NULL,
  interactive = TRUE,
  auto_update = FALSE,
  ...
)

Arguments

database_path	(character of length 1) The file path or URL to the spreadsheet with the sequence and taxonomy data, formatted as described in the database format guide. Default: NULL, prompt user if needed.
release_path	(character of length 1) The file path or URL to the git/github repository the releases are stored in. Default: NULL, prompt user if needed.
interactive	(TRUE/FALSE of length 1) Whether or not to prompt the user. This function is designed to be interactive, so TRUE is recommended. Default: TRUE.
auto_update	(TRUE/FALSE of length 1) Whether or not to allow automated edits to the source database specified by database_path. Before any edits are made, a backup of the file will be made in the same location prefixed with ".backup_". Default: FALSE.

grunwaldlab/oomycetedbtools documentation built on March 23, 2022, 6:54 a.m.