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Create new NCBI database

Source: R/db-setup-tools.R
db_create.Rd

Create a new local SQL database from downloaded files. Currently only GenBank/nucleotide/nuccore database is supported.

Usage

db_create(
  db_type = "nucleotide",
  min_length = 0,
  max_length = NULL,
  acc_filter = NULL,
  invert = FALSE,
  alt_restez_path = NULL,
  scan = FALSE
)

Arguments

db_type

character, database type

min_length

Minimum sequence length, default 0.

max_length

Maximum sequence length, default NULL.

acc_filter

Character vector; accessions to include or exclude from the database as specified by invert.

invert

Logical vector of length 1; if TRUE, accessions in acc_filter will be excluded from the database; if FALSE, only accessions in acc_filter will be included in the database. Default FALSE.

alt_restez_path

Alternative restez path if you would like to use the downloads from a different restez path.

scan

Logical vector of length 1; should the sequence file be scanned for accessions in acc_filter prior to processing? Requires zgrep to be installed (so does not work on Windows). Only used if acc_filter is not NULL and invert is FALSE. Default FALSE.

Details

All .seq.gz files are added to the database by default. A user can specify minimum/maximum sequence lengths or accession numbers to limit the sequences to be added to the database – smaller databases are faster to search. The final selection of sequences is the result of applying all filters (acc_filter, min_length, max_length) in combination.

The scan option can decrease the time needed to build a database if only a small number of sequences should be written to the database compared to the number of the sequences downloaded from GenBank; i.e., if many of the files downloaded from GenBank do not contain any sequences that should be written to the database. When set to TRUE, if a file does not contain any of the accessions in acc_filter, further processing of that file will be skipped and none of the sequences it contains will be added to the database.

Alternatively, a user can use the alt_restez_path to add the files from an alternative restez file path. For example, you may wish to have a database of all environmental sequences but then an additional smaller one of just the sequences with lengths below 100 bp. Instead of having to download all environmental sequences twice, you can generate multiple restez databases using the same downloaded files from a single restez path.

This function will not overwrite a pre-existing database. Old databases must be deleted before a new one can be created. Use db_delete() with everything=FALSE to delete an SQL database.

Connections/disconnections to the database are made automatically.

See also

Other database: count_db_ids(), db_delete(), db_download(), demo_db_create(), is_in_db(), list_db_ids()

Examples

if (FALSE) { # \dontrun{
# Example of general usage
library(restez)
restez_path_set(filepath = 'path/for/downloads/and/database')
db_download()
db_create()

# Example of using `acc_filter`
#
# Download files to temporary directory
temp_dir <- paste0(tempdir(), "/restez", collapse = "")
dir.create(temp_dir)
restez_path_set(filepath = temp_dir)
# Choose GenBank domain 20 ('unannotated'), the smallest
db_download(preselection = 20)
# Only include three accessions in database
db_create(
  acc_filter = c("AF000122", "AF000123", "AF000124")
)
list_db_ids()
db_delete()
unlink(temp_dir)
} # }