| db_download_intern {restez} | R Documentation |
Download database (internal version)
Description
Download .seq.tar files from the latest GenBank release. The
user interactively selects the parts of GenBank to download (e.g. primates,
plants, bacteria ...).
This is an internal function so the download can be wrapped in while() to
enable persistent downloading.
Usage
db_download_intern(db = "nucleotide", overwrite = FALSE, preselection = NULL)
Arguments
db |
Database type, only 'nucleotide' currently available. |
overwrite |
T/F, overwrite pre-existing downloaded files? |
preselection |
Character vector of length 1; GenBank domains to download. If not specified (default), a menu will be provided for selection. To specify, provide either a single number or a single character string of numbers separated by spaces, e.g. "19 20" for 'Phage' (19) and 'Unannotated' (20). |
Details
The downloaded files will appear in the restez filepath under downloads.
Value
T/F, if all files download correctly, TRUE else FALSE.
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release_notes(),
latest_genbank_release(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
status_class(),
stat(),
testdatadir_get()