├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore ├── CONTRIBUTING.md ├── issue_template.md ├── pull_request_template.md └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── CONTRIBUTING.md ├── CRAN-SUBMISSION ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── biomartr-tools.R ├── connection-tools.R ├── db-get-tools.R ├── db-setup-tools.R ├── download-tools.R ├── entrez-tools.R ├── extract-tools.R ├── filepath-tools.R ├── gb-get-tools.R ├── gb-setup-tools.R ├── log-tools.R ├── mock-tools.R ├── print-tools.R ├── rentrez-wrappers.R ├── restez.R ├── status-tools.R ├── test-tools.R └── wrappers.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codemeta.json ├── cran-comments.md ├── data └── record.rda ├── examples ├── count_db_ids.R ├── db_delete.R ├── demo_db_create.R ├── entrez_fetch.R ├── gb_definition_get.R ├── gb_extract.R ├── gb_fasta_get.R ├── gb_organism_get.R ├── gb_record_get.R ├── gb_sequence_get.R ├── gb_version_get.R ├── is_in_db.R ├── list_db_ids.R ├── restez_path_get.R ├── restez_ready.R └── restez_status.R ├── inst └── CITATION ├── logo.png ├── man ├── add_rcrd_log.Rd ├── cat_line.Rd ├── char.Rd ├── check_connection.Rd ├── cleanup.Rd ├── connected.Rd ├── connection_get.Rd ├── count_db_ids.Rd ├── db_create.Rd ├── db_delete.Rd ├── db_download.Rd ├── db_download_intern.Rd ├── db_sqlngths_get.Rd ├── db_sqlngths_log.Rd ├── demo_db_create.Rd ├── dir_size.Rd ├── dwnld_path_get.Rd ├── dwnld_rcrd_log.Rd ├── entrez_fasta_get.Rd ├── entrez_fetch.Rd ├── entrez_gb_get.Rd ├── extract_accession.Rd ├── extract_by_patterns.Rd ├── extract_clean_sequence.Rd ├── extract_definition.Rd ├── extract_features.Rd ├── extract_inforecpart.Rd ├── extract_keywords.Rd ├── extract_locus.Rd ├── extract_organism.Rd ├── extract_seqrecpart.Rd ├── extract_sequence.Rd ├── extract_version.Rd ├── file_download.Rd ├── filename_log.Rd ├── flatfile_read.Rd ├── gb_build.Rd ├── gb_definition_get.Rd ├── gb_df_create.Rd ├── gb_df_generate.Rd ├── gb_extract.Rd ├── gb_fasta_get.Rd ├── gb_organism_get.Rd ├── gb_record_get.Rd ├── gb_sequence_get.Rd ├── gb_sql_add.Rd ├── gb_sql_query.Rd ├── gb_version_get.Rd ├── gbrelease_check.Rd ├── gbrelease_get.Rd ├── gbrelease_log.Rd ├── has_data.Rd ├── identify_downloadable_files.Rd ├── is_in_db.Rd ├── last_add_get.Rd ├── last_dwnld_get.Rd ├── last_entry_get.Rd ├── latest_genbank_release.Rd ├── latest_genbank_release_notes.Rd ├── list_db_ids.Rd ├── message_missing.Rd ├── mock_def.Rd ├── mock_gb_df_generate.Rd ├── mock_org.Rd ├── mock_rec.Rd ├── mock_seq.Rd ├── ncbi_acc_get.Rd ├── predict_datasizes.Rd ├── print.status.Rd ├── readme_log.Rd ├── record.Rd ├── restez.Rd ├── restez_connect.Rd ├── restez_disconnect.Rd ├── restez_path_check.Rd ├── restez_path_get.Rd ├── restez_path_set.Rd ├── restez_path_unset.Rd ├── restez_ready.Rd ├── restez_rl.Rd ├── restez_status.Rd ├── search_gz.Rd ├── seshinfo_log.Rd ├── setup.Rd ├── slctn_get.Rd ├── slctn_log.Rd ├── sql_path_get.Rd ├── stat.Rd ├── status_class.Rd └── testdatadir_get.Rd ├── other ├── demonstration_1.R ├── dev.R ├── generate_records_data.R ├── make_sure_things_work.R ├── phylotar_demo.R ├── random_file_tester.R ├── rodent_build_times.rds ├── rodent_db.R ├── spell_check.R └── viral_lookup.R ├── paper ├── outline.png ├── paper.bib ├── paper.html └── paper.md ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── revdep ├── .gitignore ├── README.md ├── cran.md ├── email.yml ├── failures.md └── problems.md ├── tests ├── test-all.R └── testthat │ ├── data │ ├── records.RData │ └── release_notes_gb224.RData │ ├── test-biomartr-tools.R │ ├── test-connection-tools.R │ ├── test-db-tools.R │ ├── test-entrez-tools.R │ ├── test-extract-tools.R │ ├── test-filepath-tools.R │ ├── test-gb-setup-tools.R │ ├── 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