Man pages for ropensci/restez
Create and Query a Local Copy of 'GenBank' in R

add_rcrd_logLog files added to the SQL database in the restez path
cat_lineCat lines
charPrint green
check_connectionHelper function to test if a stable internet connection can...
cleanupClean up test data
connectedIs restez connected?
connection_getRetrieve restez connection
count_db_idsReturn the number of ids
custom_downloadHelper function to perform customized downloads
custom_download2Callr version of custom_download()
db_createCreate new NCBI database
db_deleteDelete database
db_downloadDownload database
db_sqlngths_getReturn the minimum and maximum sequence lengths in db
db_sqlngths_logLog the min and max sequence lengths
demo_db_createCreate demo database
dir_sizeCalculate the size of a directory
dwnld_path_getGet dwnld path
dwnld_rcrd_logLog a downloaded file in the restez path
entrez_fasta_getGet Entrez fasta
entrez_fetchEntrez fetch
entrez_gb_getGet Entrez GenBank record
extract_accessionExtract accession
extract_by_patternsExtract by keyword
extract_clean_sequenceExtract clean sequence from sequence part
extract_definitionExtract definition
extract_featuresExtract features
extract_inforecpartExtract the information record part
extract_keywordsExtract keywords
extract_locusExtract locus
extract_organismExtract organism
extract_seqrecpartExtract the sequence record part
extract_sequenceExtract sequence
extract_versionExtract version
file_downloadDownload a file
filename_logWrite filenames to log files
flatfile_readRead flatfile sequence records
gb_buildRead and add .seq files to database
gb_build2Callr version of gb_build()
gb_definition_getGet definition from GenBank
gb_df_createCreate GenBank data.frame
gb_df_generateGenerate GenBank records data.frame
gb_extractExtract elements of a GenBank record
gb_fasta_getGet fasta from GenBank
gb_organism_getGet organism from GenBank
gb_record_getGet record from GenBank
gbrelease_checkCheck if the last GenBank release number is the latest
gbrelease_getGet the GenBank release number in the restez path
gbrelease_logLog the GenBank release number in the restez path
gb_sequence_getGet sequence from GenBank
gb_sql_addAdd to GenBank SQL database
gb_sql_queryQuery the GenBank SQL
gb_version_getGet version from GenBank
has_dataDoes the connected database have data?
identify_downloadable_filesIdentify downloadable files
is_in_dbIs in db
last_add_getReturn date and time of the last added sequence
last_dwnld_getReturn date and time of the last download
last_entry_getReturn the last entry
latest_genbank_releaseRetrieve latest GenBank release number
latest_genbank_release_notesDownload the latest GenBank Release Notes
list_db_idsList database IDs
message_missingProduce message of missing IDs
mock_defMock def
mock_gb_df_generateGenerate mock GenBank records data.frame
mock_orgMock org
mock_recMock rec
mock_seqMock seq
predict_datasizesPrint file size predictions to screen
print.statusPrint method for status class
quiet_connectQuiely connect to the restez database
readme_logCreate README in restez_path
recordExample GenBank record
restezrestez: Create and Query a Local Copy of GenBank in R
restez_connectConnect to the restez database
restez_disconnectDisconnect from restez database
restez_path_checkCheck restez filepath
restez_path_getGet restez path
restez_path_setSet restez path
restez_path_unsetUnset restez path
restez_readyIs restez ready?
restez_rlRestez readline
restez_statusCheck restez status
seshinfo_logLog the system session information in restez path
setupSet up test common test data
slctn_getRetrieve GenBank selections made by user
slctn_logLog the GenBank selection made by a user
sql_path_getGet SQL path
statPrint blue
status_classGenerate a list class for storing status information
testdatadir_getGet test data directory
ropensci/restez documentation built on Jan. 11, 2019, 5:39 p.m.