Set-up

Set and verify your restez path

restez

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

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

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

custom_download()

Helper function to perform customized downloads

custom_download2()

Callr version of custom_download()

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_build2()

Callr version of gb_build()

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

print(<status>)

Print method for status class

quiet_connect()

Quiely connect to the restez database

readme_log()

Create README in restez_path

restez_path_check()

Check restez filepath

restez_rl()

Restez readline

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