Curate sequences from genbank — taxonomy.retrieve • phruta

After downloading sequences from genbank, this function curates sequences based on taxonomic information. Note that this function provides two summary datasets. First, the accession numbers. Second, the taxonomic information for each species in the database. The taxonomy strictly follows the gbif taxonomic backbone. The resulting files are saved to "1.CuratedSequences". The resulting files also have the most recent curated taxonomy following the gbif taxonomic backbone.

Usage

taxonomy.retrieve(
  species_names = NULL,
  database = "gbif",
  kingdom = NULL,
  ranks = c("kingdom", "phylum", "class", "order", "family", "genus", "species")
)

Arguments

species_names: A vector of species names
database: A name of a database with taxonomic information. 'gbif' only works for animals and plants. Databases follows taxize::classification
kingdom: Optional and only used when database = 'gbif'. Two possible options: "animals" or "plants."
ranks: Taxonomic ranks to retrieve from the target species.

Value

data.frame of taxonomic information for the target species (valid in the database)

Examples

if (FALSE) {
taxonomy.retrieve(
  species_names = c(
    "Felis_catus", "PREDICTED:_Vulpes",
    "Phoca_largha", "PREDICTED:_Phoca",
    "PREDICTED:_Manis", "Felis_silvestris", "Felis_nigripes"
  ),
  database = "gbif", kingdom = "animals"
)
}