Package index
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restez_path_set() - Set restez path
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restez_path_get() - Get restez path
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restez_path_unset() - Unset restez path
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restez_connect() - Connect to the restez database
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restez_disconnect() - Disconnect from restez database
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restez_status() - Check restez status
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restez_ready() - Is restez ready?
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db_create() - Create new NCBI database
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db_delete() - Delete database
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db_download() - Download database
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demo_db_create() - Create demo database
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is_in_db() - Is in db
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list_db_ids() - List database IDs
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count_db_ids() - Return the number of ids
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ncbi_acc_get() - Get accession numbers by querying NCBI GenBank
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print(<status>) - Print method for status class
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gb_definition_get() - Get definition from GenBank
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gb_fasta_get() - Get fasta from GenBank
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gb_organism_get() - Get organism from GenBank
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gb_record_get() - Get record from GenBank
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gb_sequence_get() - Get sequence from GenBank
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gb_version_get() - Get version from GenBank
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gb_extract() - Extract elements of a GenBank record
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entrez_fetch() - Entrez fetch
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record - Example GenBank record
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add_rcrd_log() - Log files added to the SQL database in the restez path
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cat_line() - Cat lines
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char() - Print green
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check_connection() - Helper function to test if a stable internet connection can be established.
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cleanup() - Clean up test data
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connected() - Is restez connected?
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connection_get() - Retrieve restez connection
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db_download_intern() - Download database (internal version)
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db_sqlngths_get() - Return the minimum and maximum sequence lengths in db
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db_sqlngths_log() - Log the min and max sequence lengths
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dir_size() - Calculate the size of a directory
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dwnld_path_get() - Get dwnld path
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dwnld_rcrd_log() - Log a downloaded file in the restez path
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entrez_fasta_get() - Get Entrez fasta
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entrez_gb_get() - Get Entrez GenBank record
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extract_accession() - Extract accession
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extract_by_patterns() - Extract by keyword
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extract_clean_sequence() - Extract clean sequence from sequence part
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extract_definition() - Extract definition
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extract_features() - Extract features
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extract_inforecpart() - Extract the information record part
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extract_keywords() - Extract keywords
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extract_locus() - Extract locus
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extract_organism() - Extract organism
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extract_seqrecpart() - Extract the sequence record part
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extract_sequence() - Extract sequence
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extract_version() - Extract version
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file_download() - Download a file
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filename_log() - Write filenames to log files
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flatfile_read() - Read flatfile sequence records
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gb_build() - Read and add .seq files to database
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gb_df_create() - Create GenBank data.frame
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gb_df_generate() - Generate GenBank records data.frame
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gb_sql_add() - Add to GenBank SQL database
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gb_sql_query() - Query the GenBank SQL
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gbrelease_check() - Check if the last GenBank release number is the latest
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gbrelease_get() - Get the GenBank release number in the restez path
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gbrelease_log() - Log the GenBank release number in the restez path
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has_data() - Does the connected database have data?
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identify_downloadable_files() - Identify downloadable files
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last_add_get() - Return date and time of the last added sequence
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last_dwnld_get() - Return date and time of the last download
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last_entry_get() - Return the last entry
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latest_genbank_release() - Retrieve latest GenBank release number
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latest_genbank_release_notes() - Download the latest GenBank Release Notes
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message_missing() - Produce message of missing IDs
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mock_def() - Mock def
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mock_gb_df_generate() - Generate mock GenBank records data.frame
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mock_org() - Mock org
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mock_rec() - Mock rec
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mock_seq() - Mock seq
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predict_datasizes() - Print file size predictions to screen
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readme_log() - Create README in restez_path
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restez_path_check() - Check restez filepath
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restez_rl() - Restez readline
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search_gz() - Scan a gzipped file for text
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seshinfo_log() - Log the system session information in restez path
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setup() - Set up test common test data
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slctn_get() - Retrieve GenBank selections made by user
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slctn_log() - Log the GenBank selection made by a user
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sql_path_get() - Get SQL path
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stat() - Print blue
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status_class() - Generate a list class for storing status information
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testdatadir_get() - Get test data directory