Recursively get lineage from OTT taxid This function derives the full lineage of a taxon ID number from a given taxonomy database

Recursively get lineage from OTT taxid This function derives the full lineage of a taxon ID number from a given taxonomy database

get_ott_lineage(
  x,
  db,
  output = "tax_name",
  ranks = c("kingdom", "phylum", "class", "order", "family", "genus", "species"),
  multithread = FALSE
)

Arguments

x

A DNAbin, DNAStringSet, taxonomy headers formnatted Acc|taxid;taxonomy, or vector of taxids

db

an OTT taxonomic database

output

Options are "tax_name" to return taxonomic names for each rank in the lineage or "tax_id" to return taxonomic ID's.

ranks

the taxonomic ranks to filter to. Default is "kingdom", "phylum", "class", "order", "family", "genus", "species" To get strain level ranks, add "terminal" to ranks

multithread

Whether multithreading should be used, if TRUE the number of cores will be automatically detected (Maximum available cores - 1), or provide a numeric vector to manually set the number of cores to use. Default is FALSE (single thread) This argument may alternatively be a 'cluster' object, in which case it is the user's responsibility to close the socket connection at the conclusion of the operation, for example by running parallel::stopCluster(cores).