db_download_intern: Download database (internal version)

In restez: Create and Query a Local Copy of 'GenBank' in R

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()

restez documentation built on Oct. 25, 2023, 5:06 p.m.