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

# Create and Query a Local Copy of 'GenBank' in R

## Documentation for package ‘restez’ version 2.1.5

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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