getAccessions: Find all accessions for a taxa
In sherrillmix/taxonomizr: Functions to Work with NCBI Accessions and Taxonomy

getAccessions

R 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)

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)

sherrillmix/taxonomizr documentation built on Jan. 26, 2024, 11:01 a.m.