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

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Documentation for package ‘restez’ version 2.1.4

• DESCRIPTION file.
• Package NEWS.

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