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 |