Get record from GenBank

Return the entire GenBank record for an accession ID. Equivalent to rettype='gb' in rentrez::entrez_fetch().

Usage

gb_record_get(id)

Arguments

id

character, sequence accession ID(s)

Value

named vector of records, if no results found NULL

See also

ncbi_acc_get()

Other get: gb_definition_get(), gb_fasta_get(), gb_organism_get(), gb_sequence_get(), gb_version_get()

Examples

library(restez)
restez_path_set(filepath = tempdir())
#> ... Creating '/tmp/RtmpWQaZTT/restez'
#> ... Creating '/tmp/RtmpWQaZTT/restez/downloads'
demo_db_create(n = 5)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpWQaZTT/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
(rec <- gb_record_get(id = 'demo_1'))
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpWQaZTT/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#>                                                                                                                                                                                                                                                                                                                                                                                                 demo_1 
#> "LOCUS       [This is a mock GenBank data record]\nDEFINITION  A demonstration sequence | id demo_1\nACCESSION   demo_1\nVERSION     2\nKEYWORDS    [keyword]\nSOURCE      [tissue, organism]\nORGANISM    Unreal organism 1\nREFERENCE   [reference data]\nAUTHORS     [all the authors]\nTITLE       [title]\nJOURNAL     [journal]\nFEATURES    [features]\n\nORIGIN      \n        1 aatactagac\n" 
(recs <- gb_record_get(id = c('demo_1', 'demo_2')))
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpWQaZTT/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#>                                                                                                                                                                                                                                                                                                                                                                                                 demo_1 
#> "LOCUS       [This is a mock GenBank data record]\nDEFINITION  A demonstration sequence | id demo_1\nACCESSION   demo_1\nVERSION     2\nKEYWORDS    [keyword]\nSOURCE      [tissue, organism]\nORGANISM    Unreal organism 1\nREFERENCE   [reference data]\nAUTHORS     [all the authors]\nTITLE       [title]\nJOURNAL     [journal]\nFEATURES    [features]\n\nORIGIN      \n        1 aatactagac\n" 
#>                                                                                                                                                                                                                                                                                                                                                                                                 demo_2 
#> "LOCUS       [This is a mock GenBank data record]\nDEFINITION  A demonstration sequence | id demo_2\nACCESSION   demo_2\nVERSION     2\nKEYWORDS    [keyword]\nSOURCE      [tissue, organism]\nORGANISM    Unreal organism 2\nREFERENCE   [reference data]\nAUTHORS     [all the authors]\nTITLE       [title]\nJOURNAL     [journal]\nFEATURES    [features]\n\nORIGIN      \n        1 gccggacttt\n" 


# delete demo after example
db_delete(everything = TRUE)