Description Usage Arguments Details Value See Also Examples
Return a vector of all IDs in a database.
1 | list_db_ids(db = "nucleotide", n = 100)
|
db |
character, database name |
n |
Maximum number of IDs to return, if NULL returns all |
Warning: can return very large vectors for large databases.
vector of characters
Other database: count_db_ids
,
db_create
, db_delete
,
db_download
, demo_db_create
,
is_in_db
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
# Warning: not recommended for real databases
# with potentially millions of IDs
restez_connect()
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)
|
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