getAccessions: Find all accessions for a taxa

View source: R/taxa.R

getAccessionsR Documentation

Find all accessions for a taxa

Description

Find accessions numbers for a given taxa ID the NCBI taxonomy. This will be pretty slow unless the database was built with indexTaxa=TRUE since the database would not have an index for taxaId.

Usage

getAccessions(taxaId, sqlFile, version = c("version", "base"), limit = NULL)

Arguments

taxaId

a vector of taxonomic IDs

sqlFile

a string giving the path to a SQLite file created by read.accession2taxid

version

either 'version' indicating that taxaids are versioned e.g. Z17427.1 or 'base' indicating that taxaids do not have version numbers e.g. Z17427

limit

return only this number of accessions or NULL for no limits

Value

a vector of character strings giving taxa IDs (potentially comma concatenated for any taxa with ambiguous names)

See Also

read.accession2taxid

Examples

taxa<-c(
  "accession\taccession.version\ttaxid\tgi",
  "Z17427\tZ17427.1\t3702\t16569",
  "Z17428\tZ17428.1\t3702\t16570",
  "Z17429\tZ17429.1\t3702\t16571",
  "Z17430\tZ17430.1\t3702\t16572"
)
inFile<-tempfile()
sqlFile<-tempfile()
writeLines(taxa,inFile)
read.accession2taxid(inFile,sqlFile,vocal=FALSE)
getAccessions(3702,sqlFile)

taxonomizr documentation built on May 29, 2024, 8:49 a.m.