list_db_ids: List database IDs
| list_db_ids | R Documentation |
List database IDs
Description
Return a vector of all IDs in a database.
Usage
list_db_ids(db = "nucleotide", n = 100)
Arguments
db |
character, database name |
n |
Maximum number of IDs to return, if NULL returns all |
Details
Warning: can return very large vectors for large databases.
Value
vector of characters
See Also
Other database:
count_db_ids(),
db_create(),
db_delete(),
db_download(),
demo_db_create(),
is_in_db()
Examples
library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
# Warning: not recommended for real databases
# with potentially millions of IDs
all_ids <- list_db_ids()
# What shall we do with these IDs?
# ... how about make a mock fasta file
seqs <- gb_sequence_get(id = all_ids)
defs <- gb_definition_get(id = all_ids)
# paste together
fasta_seqs <- paste0('>', defs, '\n', seqs)
fasta_file <- paste0(fasta_seqs, collapse = '\n')
cat(fasta_file)
# delete after example
db_delete(everything = TRUE)
