taxonomizr (version 0.2.2)

read.accession2taxid: Read NCBI accession2taxid files

Description

Take NCBI accession2taxid files, keep only accession and taxa and save it as a sqlite database

Usage

read.accession2taxid(taxaFiles, sqlFile, vocal = TRUE, extraSqlCommand = "")

Arguments

taxaFiles

a string or vector of strings giving the path(s) to files to be read in

sqlFile

a string giving the path where the output sqlite file should be saved

vocal

if TRUE output status messages

extraSqlCommand

for advanced use. A string giving a command to be called on the sqlite databse before loading data e.g. "pragma temp_store = 2;" to keep all temp files in memory (don't do this unless you have a lot (>100 Gb) of RAM)

Value

TRUE if sucessful

References

ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid

See Also

read.nodes, read.names

Examples

# NOT RUN {
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()
outFile<-tempfile()
writeLines(taxa,inFile)
read.accession2taxid(inFile,outFile)
db<-RSQLite::dbConnect(RSQLite::SQLite(),dbname=outFile)
RSQLite::dbGetQuery(db,'SELECT * FROM accessionTaxa')
# }