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Set-up

Set and verify your restez path

restez_path_set()
Set restez path
restez_path_get()
Get restez path
restez_path_unset()
Unset restez path
restez_connect()
Connect to the restez database
restez_disconnect()
Disconnect from restez database
restez_status()
Check restez status
restez_ready()
Is restez ready?

Database

Download, create, delete and verify your local database

db_create()
Create new NCBI database
db_delete()
Delete database
db_download()
Download database
demo_db_create()
Create demo database
is_in_db()
Is in db
list_db_ids()
List database IDs
count_db_ids()
Return the number of ids
ncbi_acc_get()
Get accession numbers by querying NCBI GenBank
print(<status>)
Print method for status class

GenBank

Retrieve data from the local GenBank database

gb_definition_get()
Get definition from GenBank
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_version_get()
Get version from GenBank
gb_extract()
Extract elements of a GenBank record

Entrez wrappers

Wrappers for integration with the R package rentrez

entrez_fetch()
Entrez fetch

Data

Example data

record
Example GenBank record

Internal functions

Private internal functions, documented here for openness

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
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
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_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
file_download()
Download a file
filename_log()
Write filenames to log files
flatfile_read()
Read flatfile sequence records
gb_build()
Read and add .seq files to database
gb_df_create()
Create GenBank data.frame
gb_df_generate()
Generate GenBank records data.frame
gb_sql_add()
Add to GenBank SQL database
gb_sql_query()
Query the GenBank SQL
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
has_data()
Does the connected database have data?
identify_downloadable_files()
Identify downloadable files
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
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
predict_datasizes()
Print file size predictions to screen
readme_log()
Create README in restez_path
restez_path_check()
Check restez filepath
restez_rl()
Restez readline
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