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 (default: 'version')
- 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)
#> taxa accession
#> 1 3702 Z17427.1
#> 2 3702 Z17428.1
#> 3 3702 Z17429.1
#> 4 3702 Z17430.1