Package: restez 2.1.4.9000

Joel H. Nitta

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

Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers.

Authors:Joel H. Nitta [aut, cre], Dom Bennett [aut]

restez_2.1.4.9000.tar.gz
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restez.pdf |restez.html✨
restez/json (API)
NEWS

# Install 'restez' in R:
install.packages('restez', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/restez/issues

Pkgdown:https://docs.ropensci.org

Datasets:
  • record - Example GenBank record

On CRAN:

dnaentrezgenbanksequence

6.55 score 25 stars 1 packages 191 scripts 246 downloads 23 exports 22 dependencies

Last updated 8 months agofrom:1e5c917120 (on main). Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 27 2024
R-4.5-winOKNov 27 2024
R-4.5-linuxOKNov 27 2024
R-4.4-winOKNov 27 2024
R-4.4-macOKNov 27 2024
R-4.3-winOKNov 27 2024
R-4.3-macOKNov 27 2024

Exports:count_db_idsdb_createdb_deletedb_downloaddemo_db_createentrez_fetchgb_definition_getgb_extractgb_fasta_getgb_organism_getgb_record_getgb_sequence_getgb_version_getis_in_dblist_db_idsncbi_acc_getrestez_connectrestez_disconnectrestez_path_getrestez_path_setrestez_path_unsetrestez_readyrestez_status

Dependencies:apeaskpassassertthatclicrayoncurlDBIdigestduckdbfshttrjsonlitelatticemimenlmeopensslR6RcpprentrezstringisysXML

Readme and manuals

Help Manual

Help pageTopics
Log files added to the SQL database in the restez pathadd_rcrd_log
Cat linescat_line
Print greenchar
Helper function to test if a stable internet connection can be established.check_connection
Clean up test datacleanup
Is restez connected?connected
Retrieve restez connectionconnection_get
Return the number of idscount_db_ids
Create new NCBI databasedb_create
Delete databasedb_delete
Download databasedb_download
Download database (internal version)db_download_intern
Return the minimum and maximum sequence lengths in dbdb_sqlngths_get
Log the min and max sequence lengthsdb_sqlngths_log
Create demo databasedemo_db_create
Calculate the size of a directorydir_size
Get dwnld pathdwnld_path_get
Log a downloaded file in the restez pathdwnld_rcrd_log
Get Entrez fastaentrez_fasta_get
Entrez fetchentrez_fetch
Get Entrez GenBank recordentrez_gb_get
Extract accessionextract_accession
Extract by keywordextract_by_patterns
Extract clean sequence from sequence partextract_clean_sequence
Extract definitionextract_definition
Extract featuresextract_features
Extract the information record partextract_inforecpart
Extract keywordsextract_keywords
Extract locusextract_locus
Extract organismextract_organism
Extract the sequence record partextract_seqrecpart
Extract sequenceextract_sequence
Extract versionextract_version
Download a filefile_download
Write filenames to log filesfilename_log
Read flatfile sequence recordsflatfile_read
Read and add .seq files to databasegb_build
Get definition from GenBankgb_definition_get
Create GenBank data.framegb_df_create
Generate GenBank records data.framegb_df_generate
Extract elements of a GenBank recordgb_extract
Get fasta from GenBankgb_fasta_get
Get organism from GenBankgb_organism_get
Get record from GenBankgb_record_get
Get sequence from GenBankgb_sequence_get
Add to GenBank SQL databasegb_sql_add
Query the GenBank SQLgb_sql_query
Get version from GenBankgb_version_get
Check if the last GenBank release number is the latestgbrelease_check
Get the GenBank release number in the restez pathgbrelease_get
Log the GenBank release number in the restez pathgbrelease_log
Does the connected database have data?has_data
Identify downloadable filesidentify_downloadable_files
Is in dbis_in_db
Return date and time of the last added sequencelast_add_get
Return date and time of the last downloadlast_dwnld_get
Return the last entrylast_entry_get
Retrieve latest GenBank release numberlatest_genbank_release
Download the latest GenBank Release Noteslatest_genbank_release_notes
List database IDslist_db_ids
Produce message of missing IDsmessage_missing
Mock defmock_def
Generate mock GenBank records data.framemock_gb_df_generate
Mock orgmock_org
Mock recmock_rec
Mock seqmock_seq
Get accession numbers by querying NCBI GenBankncbi_acc_get
Print file size predictions to screenpredict_datasizes
Print method for status classprint.status
Create README in restez_pathreadme_log
Example GenBank recordrecord
Connect to the restez databaserestez_connect
Disconnect from restez databaserestez_disconnect
Check restez filepathrestez_path_check
Get restez pathrestez_path_get
Set restez pathrestez_path_set
Unset restez pathrestez_path_unset
Is restez ready?restez_ready
Restez readlinerestez_rl
Check restez statusrestez_status
Scan a gzipped file for textsearch_gz
Log the system session information in restez pathseshinfo_log
Set up test common test datasetup
Retrieve GenBank selections made by userslctn_get
Log the GenBank selection made by a userslctn_log
Get SQL pathsql_path_get
Print bluestat
Generate a list class for storing status informationstatus_class
Get test data directorytestdatadir_get