prepareDatabase | R Documentation |
Convenience function to do all necessary preparations downloading names, nodes and accession2taxid data from NCBI and preprocessing into a SQLite database for downstream use.
prepareDatabase( sqlFile = "nameNode.sqlite", tmpDir = ".", getAccessions = TRUE, vocal = TRUE, ... )
sqlFile |
character string giving the file location to store the SQLite database |
tmpDir |
location for storing the downloaded files from NCBI. (Note that it may be useful to store these somewhere convenient to avoid redownloading) |
getAccessions |
if TRUE download the very large accesssion2taxid files necessary to convert accessions to taxonomic IDs |
vocal |
if TRUE output messages describing progress |
... |
Arguments passed on to
|
a vector of character string giving the path to the SQLite file
getNamesAndNodes
, getAccession2taxid
, read.accession2taxid
, read.nodes.sql
, read.names.sql
## Not run: if(readline( "This will download a lot data and take a while to process. Make sure you have space and bandwidth. Type y to continue: " )!='y') stop('This is a stop to make sure no one downloads a bunch of data unintentionally') prepareDatabase() ## End(Not run)
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