ncbi_acc_get {restez} | R Documentation |
Get accession numbers by querying NCBI GenBank
Description
The query string can be formatted using GenBank advanced query terms to obtain accession numbers corresponding to a specific set of criteria.
Usage
ncbi_acc_get(query, strict = TRUE, drop_ver = TRUE)
Arguments
query |
Character vector of length 1; query string to search GenBank. |
strict |
Logical vector of length 1; should an error be issued if the number of unique accessions retrieved does not match the number of hits from GenBank? Default TRUE. |
drop_ver |
Logical vector of length 1; should the version part of the accession number (e.g., '.1' in 'AB001538.1') be dropped? Default TRUE. |
Details
Note this queries NCBI GenBank, not the local database generated with restez.
It can be used either to restrict the accessions used to construct the local
database (acc_filter
argument of db_create()
) or to specify accessions
to read from the local database (id
argument of gb_fasta_get()
and other
gb_*_get() functions).
Value
Character vector; accession numbers resulting from query.
See Also
Examples
## Not run:
# requires an internet connection
cmin_accs <- ncbi_acc_get("Crepidomanes minutum")
length(cmin_accs)
head(cmin_accs)
## End(Not run)