| Type: | Package |
| Title: | Create and Query a Local Copy of 'GenBank' in R |
| Version: | 2.1.5 |
| Maintainer: | Joel H. Nitta <joelnitta@gmail.com> |
| Description: | 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. |
| URL: | https://github.com/ropensci/restez, https://docs.ropensci.org/restez/ |
| BugReports: | https://github.com/ropensci/restez/issues |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| Depends: | R (≥ 3.3.0) |
| Imports: | utils, rentrez, DBI (≥ 1.0.0), curl, cli, crayon, stringi, duckdb, fs, assertthat, ape |
| Suggests: | sessioninfo, testthat, knitr, R.utils, rmarkdown, mockery |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2025-03-06 23:44:02 UTC; joelnitta |
| Author: | Joel H. Nitta 
[aut, cre],
Dom Bennett [aut] |
| Repository: | CRAN |
| Date/Publication: | 2025-03-07 00:00:02 UTC |
restez: Create and Query a Local Copy of GenBank in R
Description
The restez package comes with five families of functions: setup, database, get, entrez and internal/private.
Setup functions
These functions allow a user to set the filepath for where the GenBank files should be stored, create connections and verify these settings.
Database functions
These functions download specific parts of GenBank and create the local SQL-like database.
GenBank functions
These functions allow a user to query the local SQL-like database. A user can use an NCBI accession ID to retrieve sequences or whole GenBank records.
Entrez functions
The entrez functions are wrappers to the entrez_* functions in the
rentrez package. e.g the restez's entrez_fetch will first try to search the
local database, if it fails it will then call rentrez's
rentrez::entrez_fetch() with the same arguments.
Private/internal functions
These functions work behind the scenes to make everything work. If you're
curious you can read their documentation using the form
?restez:::functionname.
Author(s)
Maintainer: Joel H. Nitta joelnitta@gmail.com (ORCID)
Authors:
Dom Bennett dominic.john.bennett@gmail.com (ORCID)
See Also
Useful links:
Report bugs at https://github.com/ropensci/restez/issues
Log files added to the SQL database in the restez path
Description
This function is called whenever sequence files have been successfully added to the nucleotide SQL database. Row entries are added to 'add_lot.tsv' in the user's restez path containing the filename, GB release numbers and the time of successful adding. The log is to help users keep track of when sequences have been added.
Usage
add_rcrd_log(fl)
Arguments
fl |
filename, character |
See Also
Other private:
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Cat lines
Description
Helper function for printing lines to console. Automatically formats lines by adding newlines.
Usage
cat_line(...)
Arguments
... |
Text to print, character |
See Also
Other private:
add_rcrd_log(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Print green
Description
Print to console green text to indicate a name/filepath/text
Usage
char(x)
Arguments
x |
Text to print, character |
Value
coloured character encoding, character
See Also
Other private:
add_rcrd_log(),
cat_line(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Helper function to test if a stable internet connection can be established.
Description
All retrieval functions need a stable internet connection to work properly. This internal function pings the google homepage and throws an error if it cannot be reached.
Usage
check_connection()
Author(s)
Hajk-Georg Drost
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Clean up test data
Description
Removes all temporary test data created.
Usage
cleanup()
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Is restez connected?
Description
Returns TRUE if a restez SQL database has been connected.
Usage
connected()
Value
Logical
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Retrieve restez connection
Description
Safely acquire the restez connection. Raises error if no connection set.
Usage
connection_get()
Value
connection
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Return the number of ids
Description
Return the number of ids in a user's restez database.
Usage
count_db_ids(db = "nucleotide")
Arguments
db |
character, database name |
Details
Requires an open connection. If no connection or db 0 is returned.
Value
integer
See Also
Other database:
db_create(),
db_delete(),
db_download(),
demo_db_create(),
is_in_db(),
list_db_ids()
Examples
library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
(count_db_ids())
# delete demo after example
db_delete(everything = TRUE)
Create new NCBI database
Description
Create a new local SQL database from downloaded files. Currently only GenBank/nucleotide/nuccore database is supported.
Usage
db_create(
db_type = "nucleotide",
min_length = 0,
max_length = NULL,
acc_filter = NULL,
invert = FALSE,
alt_restez_path = NULL,
scan = FALSE
)
Arguments
db_type |
character, database type |
min_length |
Minimum sequence length, default 0. |
max_length |
Maximum sequence length, default NULL. |
acc_filter |
Character vector; accessions to include or exclude from
the database as specified by |
invert |
Logical vector of length 1; if TRUE, accessions in |
alt_restez_path |
Alternative restez path if you would like to use the downloads from a different restez path. |
scan |
Logical vector of length 1; should the sequence file be scanned
for accessions in |
Details
All .seq.gz files are added to the database by default. A user can specify
minimum/maximum sequence lengths or accession numbers to limit the sequences
to be added to the database – smaller databases are faster to search. The
final selection of sequences is the result of applying all filters
(acc_filter, min_length, max_length) in combination.
The scan option can decrease the time needed to build a database if only a
small number of sequences should be written to the database compared to the
number of the sequences downloaded from GenBank; i.e., if many of the files
downloaded from GenBank do not contain any sequences that should be written
to the database. When set to TRUE, if a file does not contain any of the
accessions in acc_filter, further processing of that file will be skipped
and none of the sequences it contains will be added to the database.
Alternatively, a user can use the alt_restez_path to add the files
from an alternative restez file path. For example, you may wish to have a
database of all environmental sequences but then an additional smaller one of
just the sequences with lengths below 100 bp. Instead of having to download
all environmental sequences twice, you can generate multiple restez databases
using the same downloaded files from a single restez path.
This function will not overwrite a pre-existing database. Old databases must
be deleted before a new one can be created. Use db_delete() with
everything=FALSE to delete an SQL database.
Connections/disconnections to the database are made automatically.
See Also
Other database:
count_db_ids(),
db_delete(),
db_download(),
demo_db_create(),
is_in_db(),
list_db_ids()
Examples
## Not run:
# Example of general usage
library(restez)
restez_path_set(filepath = 'path/for/downloads/and/database')
db_download()
db_create()
# Example of using `acc_filter`
#
# Download files to temporary directory
temp_dir <- paste0(tempdir(), "/restez", collapse = "")
dir.create(temp_dir)
restez_path_set(filepath = temp_dir)
# Choose GenBank domain 20 ('unannotated'), the smallest
db_download(preselection = 20)
# Only include three accessions in database
db_create(
acc_filter = c("AF000122", "AF000123", "AF000124")
)
list_db_ids()
db_delete()
unlink(temp_dir)
## End(Not run)
Delete database
Description
Delete the local SQL database and/or restez folder.
Usage
db_delete(everything = FALSE)
Arguments
everything |
T/F, delete the whole restez folder as well? |
Details
Any connected database will be automatically disconnected.
See Also
Other database:
count_db_ids(),
db_create(),
db_download(),
demo_db_create(),
is_in_db(),
list_db_ids()
Examples
library(restez)
fp <- tempdir()
restez_path_set(filepath = fp)
demo_db_create(n = 10)
db_delete(everything = FALSE)
# Will not run: gb_sequence_get(id = 'demo_1')
# only the SQL database is deleted
db_delete(everything = TRUE)
# Now returns NULL
(restez_path_get())
Download database
Description
Download .seq.tar files from the latest GenBank release.
Usage
db_download(
db = "nucleotide",
overwrite = FALSE,
preselection = NULL,
max_tries = 1
)
Arguments
db |
Database type, only 'nucleotide' currently available. |
overwrite |
T/F, overwrite pre-existing downloaded files? |
preselection |
Character vector of length 1; GenBank domains to download. If not specified (default), a menu will be provided for selection. To specify, provide either a single number or a single character string of numbers separated by spaces, e.g. "19 20" for 'Phage' (19) and 'Unannotated' (20). |
max_tries |
Numeric vector of length 1; maximum number of times to attempt downloading database (default 1). |
Details
In default mode, the user interactively selects the parts (i.e., "domains")
of GenBank to download (e.g. primates, plants, bacteria ...). Alternatively,
the selected domains can be provided as a character string to preselection.
The max_tries argument is useful for large databases that may otherwise
fail due to periodic lapses in internet connectivity. This value can be set
to Inf to continuously try until the database download succeeds (not
recommended if you do not have an internet connection!).
Value
T/F, if all files download correctly, TRUE else FALSE.
See Also
Other database:
count_db_ids(),
db_create(),
db_delete(),
demo_db_create(),
is_in_db(),
list_db_ids()
Examples
## Not run:
library(restez)
restez_path_set(filepath = 'path/for/downloads')
db_download()
## End(Not run)
Download database (internal version)
Description
Download .seq.tar files from the latest GenBank release. The
user interactively selects the parts of GenBank to download (e.g. primates,
plants, bacteria ...).
This is an internal function so the download can be wrapped in while() to
enable persistent downloading.
Usage
db_download_intern(db = "nucleotide", overwrite = FALSE, preselection = NULL)
Arguments
db |
Database type, only 'nucleotide' currently available. |
overwrite |
T/F, overwrite pre-existing downloaded files? |
preselection |
Character vector of length 1; GenBank domains to download. If not specified (default), a menu will be provided for selection. To specify, provide either a single number or a single character string of numbers separated by spaces, e.g. "19 20" for 'Phage' (19) and 'Unannotated' (20). |
Details
The downloaded files will appear in the restez filepath under downloads.
Value
T/F, if all files download correctly, TRUE else FALSE.
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Return the minimum and maximum sequence lengths in db
Description
Returns the maximum and minimum sequence lengths as set by the user upon db creation.
Usage
db_sqlngths_get()
Details
If no file found, returns empty character vector.
Value
vector of integers
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Log the min and max sequence lengths
Description
Log the min and maximum sequence length used in the created db.
Usage
db_sqlngths_log(min_lngth, max_lngth)
Arguments
min_lngth |
Minimum length |
max_lngth |
Maximum length |
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Create demo database
Description
Creates a local mock SQL database from package test data for demonstration purposes. No internet connection required.
Usage
demo_db_create(db_type = "nucleotide", n = 100)
Arguments
db_type |
character, database type |
n |
integer, number of mock sequences |
See Also
Other database:
count_db_ids(),
db_create(),
db_delete(),
db_download(),
is_in_db(),
list_db_ids()
Examples
library(restez)
# set the restez path to a temporary dir
restez_path_set(filepath = tempdir())
# create demo database
demo_db_create(n = 5)
# in the demo, IDs are 'demo_1', 'demo_2' ...
(gb_sequence_get(id = 'demo_1'))
# Delete a demo database after an example
db_delete(everything = TRUE)
Calculate the size of a directory
Description
Returns the size of directory in GB
Usage
dir_size(fp)
Arguments
fp |
File path, character |
Value
numeric
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Get dwnld path
Description
Return path to folder where raw .seq files are stored.
Usage
dwnld_path_get()
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Log a downloaded file in the restez path
Description
This function is called whenever a file is successfully downloaded. A row entry is added to the 'download_log.tsv' in the user's restez path containing the file name, the GB release number and the time of successfully download. The log is to help users keep track of when they downloaded files and to determine if the downloaded files are out of date.
Usage
dwnld_rcrd_log(fl)
Arguments
fl |
file name, character |
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Get Entrez fasta
Description
Return fasta format as expected from an Entrez call. If not all IDs are returned, will run rentrez::entrez_fetch.
Usage
entrez_fasta_get(id, ...)
Arguments
id |
vector, unique ID(s) for record(s) |
... |
arguments passed on to rentrez |
Value
character string containing the file created
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Entrez fetch
Description
Wrapper for rentrez::entrez_fetch.
Usage
entrez_fetch(db, id = NULL, rettype, retmode = "", ...)
Arguments
db |
character, name of the database |
id |
vector, unique ID(s) for record(s) |
rettype |
character, data format |
retmode |
character, data mode |
... |
Arguments to be passed on to rentrez |
Details
Attempts to first search local database with user-specified parameters, if the record is missing in the database, the function then calls rentrez::entrez_fetch to search GenBank remotely.
rettype='fasta' and rettype='gb' are respectively equivalent to
gb_fasta_get() and gb_record_get().
Value
character string containing the file created
Supported return types and modes
XML retmode is not supported. Rettypes 'seqid', 'ft', 'acc' and 'uilist' are also not supported.
Note
It is advisable to call restez and rentrez functions with '::' notation rather than library() calls to avoid namespace issues. e.g. restez::entrez_fetch().
See Also
Examples
library(restez)
restez_path_set(tempdir())
demo_db_create(n = 5)
# return fasta record
fasta_res <- entrez_fetch(db = 'nucleotide',
id = c('demo_1', 'demo_2'),
rettype = 'fasta')
cat(fasta_res)
# return whole GB record in text format
gb_res <- entrez_fetch(db = 'nucleotide',
id = c('demo_1', 'demo_2'),
rettype = 'gb')
cat(gb_res)
# NOT RUN
# whereas these request would go through rentrez
# fasta_res <- entrez_fetch(db = 'nucleotide',
# id = c('S71333', 'S71334'),
# rettype = 'fasta')
# gb_res <- entrez_fetch(db = 'nucleotide',
# id = c('S71333', 'S71334'),
# rettype = 'gb')
# delete demo after example
db_delete(everything = TRUE)
Get Entrez GenBank record
Description
Return gb and gbwithparts format as expected from an Entrez call. If not all IDs are returned, will run rentrez::entrez_fetch.
Usage
entrez_gb_get(id, ...)
Arguments
id |
vector, unique ID(s) for record(s) |
... |
arguments passed on to rentrez |
Value
character string containing the file created
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract accession
Description
Return accession ID from GenBank record
Usage
extract_accession(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, ” returned.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract by keyword
Description
Search through GenBank record for a keyword and return text up to the end_pattern.
Usage
extract_by_patterns(record, start_pattern, end_pattern = "\n")
Arguments
record |
GenBank record in text format, character |
start_pattern |
REGEX pattern indicating the point to start extraction, character |
end_pattern |
REGEX pattern indicating the point to stop extraction, character |
Details
The start_pattern should be any of the capitalized elements in a GenBank record (e.g. LOCUS, DESCRIPTION, ACCESSION). The end_pattern depends on how much of the selected element a user wants returned. By default, the extraction will stop at the next newline. If keyword or end pattern not found, returns NULL.
Value
character or NULL
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract clean sequence from sequence part
Description
Return clean sequence from seqrecpart of a GenBank record
Usage
extract_clean_sequence(seqrecpart, max_len = 1e+08)
Arguments
seqrecpart |
Sequence part of a GenBank record, character |
max_len |
Number: maximum number of characters allowed in a single record before splitting the record into parts. Does not affect output, but only internal calculations, so generally should not be changed. Default = 1e8. |
Details
If element is not found, ” returned.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract definition
Description
Return definition from GenBank record.
Usage
extract_definition(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, ” returned.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract features
Description
Return feature table as list from GenBank record
Usage
extract_features(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, empty list returned.
Value
list of lists
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract the information record part
Description
Return information part from GenBank record
Usage
extract_inforecpart(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, ” returned.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract keywords
Description
Return keywords as list from GenBank record
Usage
extract_keywords(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, ” returned.
Value
character vector
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract locus
Description
Return locus information from GenBank record
Usage
extract_locus(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, ” returned.
Value
named character vector
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract organism
Description
Return organism name from GenBank record
Usage
extract_organism(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, ” returned.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract the sequence record part
Description
Return sequence part from GenBank record
Usage
extract_seqrecpart(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, ” returned.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract sequence
Description
Return sequence from GenBank record
Usage
extract_sequence(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, ” returned.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract version
Description
Return accession + version ID from GenBank record
Usage
extract_version(record)
Arguments
record |
GenBank record in text format, character |
Details
If element is not found, ” returned.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Download a file
Description
Download a GenBank .seq.tar file. Check the file has downloaded properly. If not, returns FALSE. If overwrite is true, any previous file will be overwritten.
Usage
file_download(fl, overwrite = FALSE)
Arguments
fl |
character, base filename (e.g. gbpri9.seq) to be downloaded |
overwrite |
T/F |
Value
T/F
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Write filenames to log files
Description
Record a filename in a log file along with GB release and time.
Usage
filename_log(fl, fp)
Arguments
fl |
file name, character |
fp |
filepath to log file, character |
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Read flatfile sequence records
Description
Read records from a .seq file.
Usage
flatfile_read(flpth)
Arguments
flpth |
Path to .seq file |
Value
list of GenBank records in text format
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Read and add .seq files to database
Description
Given a list of seq_files, read and add the contents of the files to a SQL-like database. If any errors during the process, FALSE is returned.
Usage
gb_build(
dpth,
seq_files,
max_length,
min_length,
acc_filter = NULL,
invert = FALSE,
scan = FALSE
)
Arguments
dpth |
Download path (where seq_files are stored) |
seq_files |
.seq.tar seq file names |
max_length |
Maximum sequence length, default NULL. |
min_length |
Minimum sequence length, default 0. |
acc_filter |
Character vector; accessions to include or exclude from
the database as specified by |
invert |
Logical vector of length 1; if TRUE, accessions in |
scan |
Logical vector of length 1; should the sequence file be scanned
for accessions in |
Details
This function will automatically connect to the restez database.
Value
Logical
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Get definition from GenBank
Description
Return the definition line for an accession ID.
Usage
gb_definition_get(id)
Arguments
id |
character, sequence accession ID(s) |
Value
named vector of definitions, if no results found NULL
See Also
Other get:
gb_fasta_get(),
gb_organism_get(),
gb_record_get(),
gb_sequence_get(),
gb_version_get()
Examples
library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
(def <- gb_definition_get(id = 'demo_1'))
(defs <- gb_definition_get(id = c('demo_1', 'demo_2')))
# delete demo after example
db_delete(everything = TRUE)
Create GenBank data.frame
Description
Make data.frame from columns vectors for nucleotide entries. As part of gb_df_generate().
Usage
gb_df_create(accessions, versions, organisms, definitions, sequences, records)
Arguments
accessions |
character, vector of accessions |
versions |
character, vector of accessions + versions |
organisms |
character, vector of organism names |
definitions |
character, vector of sequence definitions |
sequences |
character, vector of sequences |
records |
character, vector of GenBank records in text format |
Value
data.frame
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Generate GenBank records data.frame
Description
For a list of records, construct a data.frame for insertion into SQL database.
Usage
gb_df_generate(
records,
min_length = 0,
max_length = NULL,
acc_filter = NULL,
invert = FALSE
)
Arguments
records |
character, vector of GenBank records in text format |
min_length |
Minimum sequence length, default 0. |
max_length |
Maximum sequence length, default NULL. |
acc_filter |
Character vector; accessions to include or exclude from
the database as specified by |
invert |
Logical vector of length 1; if TRUE, accessions in |
Details
The resulting data.frame has five columns: accession, organism, raw_definition, raw_sequence, raw_record. The prefix 'raw_' indicates the data has been converted to the raw format, see ?charToRaw, in order to save on RAM. The raw_record contains the entire GenBank record in text format.
Use acc_filter and max and min sequence lengths to minimize the size of the
database. All sequences have to be at least as long as min and less than or
equal in length to max, unless max is NULL in which there is no maximum
length. The final selection of sequences is the result of applying all
filters (acc_filter, min_length, max_length) in combination.
Value
data.frame, or NULL if no records pass filters
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Extract elements of a GenBank record
Description
Return elements of GenBank record e.g. sequence, definition ...
Usage
gb_extract(
record,
what = c("accession", "version", "organism", "sequence", "definition", "locus",
"features", "keywords")
)
Arguments
record |
GenBank record in text format, character |
what |
Which element to extract |
Details
This function uses a REGEX to extract particular elements of a GenBank record. All of the what options return a single character with the exception of 'locus' or 'keywords' that return character vectors and 'features' that returns a list of lists for all features.
The accuracy of these functions cannot be guaranteed due to the enormity of the GenBank database. But the function is regularly tested on a range of GenBank records.
Note: all non-latin1 characters are converted to '-'.
Value
character or list of lists (what='features') or named character vector (what='locus')
Examples
library(restez)
data('record')
(gb_extract(record = record, what = 'locus'))
Get fasta from GenBank
Description
Get sequence and definition data in FASTA format. Equivalent to
rettype='fasta' in rentrez::entrez_fetch().
Usage
gb_fasta_get(id, width = 70)
Arguments
id |
character, sequence accession ID(s) |
width |
integer, maximum number of characters in a line |
Value
named vector of fasta sequences, if no results found NULL
See Also
Other get:
gb_definition_get(),
gb_organism_get(),
gb_record_get(),
gb_sequence_get(),
gb_version_get()
Examples
library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
(fasta <- gb_fasta_get(id = 'demo_1'))
(fastas <- gb_fasta_get(id = c('demo_1', 'demo_2')))
# delete demo after example
db_delete(everything = TRUE)
Get organism from GenBank
Description
Return the organism name for an accession ID.
Usage
gb_organism_get(id)
Arguments
id |
character, sequence accession ID(s) |
Value
named vector of definitions, if no results found NULL
See Also
Other get:
gb_definition_get(),
gb_fasta_get(),
gb_record_get(),
gb_sequence_get(),
gb_version_get()
Examples
library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
(org <- gb_organism_get(id = 'demo_1'))
(orgs <- gb_organism_get(id = c('demo_1', 'demo_2')))
# delete demo after example
db_delete(everything = TRUE)
Get record from GenBank
Description
Return the entire GenBank record for an accession ID.
Equivalent to rettype='gb' in rentrez::entrez_fetch().
Usage
gb_record_get(id)
Arguments
id |
character, sequence accession ID(s) |
Value
named vector of records, if no results found NULL
See Also
Other get:
gb_definition_get(),
gb_fasta_get(),
gb_organism_get(),
gb_sequence_get(),
gb_version_get()
Examples
library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
(rec <- gb_record_get(id = 'demo_1'))
(recs <- gb_record_get(id = c('demo_1', 'demo_2')))
# delete demo after example
db_delete(everything = TRUE)
Get sequence from GenBank
Description
Return the sequence(s) for a record(s) from the accession ID(s).
Usage
gb_sequence_get(id, dnabin = FALSE)
Arguments
id |
character, sequence accession ID(s) |
dnabin |
Logical vector of length 1; should the sequences be returned using the bit-level coding scheme of the ape package? Default FALSE. |
Details
For more information about the dnabin format, see ape::DNAbin().
Value
named vector of sequences, if no results found NULL
See Also
Other get:
gb_definition_get(),
gb_fasta_get(),
gb_organism_get(),
gb_record_get(),
gb_version_get()
Examples
library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
(seq <- gb_sequence_get(id = 'demo_1'))
(seqs <- gb_sequence_get(id = c('demo_1', 'demo_2')))
(fasta_dnabin <- gb_sequence_get(id = 'demo_1', dnabin = TRUE))
# delete demo after example
db_delete(everything = TRUE)
Add to GenBank SQL database
Description
Add records data.frame to SQL-like database.
Usage
gb_sql_add(df)
Arguments
df |
Records data.frame |
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Query the GenBank SQL
Description
Generic query function for retrieving data from the SQL database for the get functions.
Usage
gb_sql_query(nm, id)
Arguments
nm |
character, column name |
id |
character, sequence accession ID(s) |
Value
data.frame
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Get version from GenBank
Description
Return the accession version for an accession ID.
Usage
gb_version_get(id)
Arguments
id |
character, sequence accession ID(s) |
Value
named vector of versions, if no results found NULL
See Also
Other get:
gb_definition_get(),
gb_fasta_get(),
gb_organism_get(),
gb_record_get(),
gb_sequence_get()
Examples
library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
(ver <- gb_version_get(id = 'demo_1'))
(vers <- gb_version_get(id = c('demo_1', 'demo_2')))
# delete demo after example
db_delete(everything = TRUE)
Check if the last GenBank release number is the latest
Description
Returns TRUE if the GenBank release number is the most recent GenBank release available.
Usage
gbrelease_check()
Value
logical
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Get the GenBank release number in the restez path
Description
Returns the GenBank release number. Returns empty character if none found.
Usage
gbrelease_get()
Details
If no file found, returns empty character vector.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Log the GenBank release number in the restez path
Description
This function is called whenever db_download is run. It logs the GB release number in the 'gb_release.txt' in the user's restez path. The log is to help users keep track of whether their database if out of date.
Usage
gbrelease_log(release)
Arguments
release |
GenBank release number, character |
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Does the connected database have data?
Description
Returns TRUE if a restez SQL database has data.
Usage
has_data()
Value
Logical
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Identify downloadable files
Description
Searches through the release notes for a GenBank release to find all listed .seq files. Returns a data.frame for all .seq files and their description.
Usage
identify_downloadable_files()
Value
data.frame
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Is in db
Description
Determine whether an id(s) is/are present in a database.
Usage
is_in_db(id, db = "nucleotide")
Arguments
id |
character, sequence accession ID(s) |
db |
character, database name |
Value
named vector of booleans
See Also
Other database:
count_db_ids(),
db_create(),
db_delete(),
db_download(),
demo_db_create(),
list_db_ids()
Examples
library(restez)
# set the restez path to a temporary dir
restez_path_set(filepath = tempdir())
# create demo database
demo_db_create(n = 5)
# in the demo, IDs are 'demo_1', 'demo_2' ...
ids <- c('thisisnotanid', 'demo_1', 'demo_2')
(is_in_db(id = ids))
# delete demo after example
db_delete(everything = TRUE)
Return date and time of the last added sequence
Description
Return the date and time of the last added sequence as determined using the 'add_log.tsv'.
Usage
last_add_get()
Details
If no file found, returns empty character vector.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Return date and time of the last download
Description
Return the date and time of the last download as determined using the 'download_log.tsv'.
Usage
last_dwnld_get()
Details
If no file found, returns empty character vector.
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Return the last entry
Description
Return the last entry from a tab-delimited log file.
Usage
last_entry_get(fp)
Arguments
fp |
Filepath, character |
Value
vector
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Retrieve latest GenBank release number
Description
Downloads the latest GenBank release number and returns it.
Usage
latest_genbank_release()
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Download the latest GenBank Release Notes
Description
Downloads the latest GenBank release notes to a user's restez download path.
Usage
latest_genbank_release_notes()
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
List database IDs
Description
Return a vector of all IDs in a database.
Usage
list_db_ids(db = "nucleotide", n = 100)
Arguments
db |
character, database name |
n |
Maximum number of IDs to return, if NULL returns all |
Details
Warning: can return very large vectors for large databases.
Value
vector of characters
See Also
Other database:
count_db_ids(),
db_create(),
db_delete(),
db_download(),
demo_db_create(),
is_in_db()
Examples
library(restez)
restez_path_set(filepath = tempdir())
demo_db_create(n = 5)
# Warning: not recommended for real databases
# with potentially millions of IDs
all_ids <- list_db_ids()
# What shall we do with these IDs?
# ... how about make a mock fasta file
seqs <- gb_sequence_get(id = all_ids)
defs <- gb_definition_get(id = all_ids)
# paste together
fasta_seqs <- paste0('>', defs, '\n', seqs)
fasta_file <- paste0(fasta_seqs, collapse = '\n')
cat(fasta_file)
# delete after example
db_delete(everything = TRUE)
Produce message of missing IDs
Description
Sends message to console stating number of missing IDs.
Usage
message_missing(n)
Arguments
n |
Number of missing IDs |
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Mock def
Description
Make a mock sequence definition. Designed to be part of a loop.
Usage
mock_def(i)
Arguments
i |
integer, iterator |
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Generate mock GenBank records data.frame
Description
Make a mock nucleotide data.frame for entry into a demonstration SQL database.
Usage
mock_gb_df_generate(n)
Arguments
n |
integer, number of entries |
Value
data.frame
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Mock org
Description
Make a mock sequence organism. Designed to be part of a loop.
Usage
mock_org(i)
Arguments
i |
integer, iterator |
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Mock rec
Description
Create a mock GenBank record for demo-ing and testing purposes. Designed to be part of a loop. Accession, organism... etc. are optional arguments.
Usage
mock_rec(
i,
definition = NULL,
accession = NULL,
version = NULL,
organism = NULL,
sequence = NULL
)
Arguments
i |
integer, iterator |
definition |
character |
accession |
character |
version |
character |
organism |
character |
sequence |
character |
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Mock seq
Description
Make a mock sequence. Designed to be part of a loop.
Usage
mock_seq(i, sqlngth = 10)
Arguments
i |
integer, iterator |
sqlngth |
integer, sequence length |
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Get accession numbers by querying NCBI GenBank
Description
The query string can be formatted using GenBank advanced query terms to obtain accession numbers corresponding to a specific set of criteria.
Usage
ncbi_acc_get(query, strict = TRUE, drop_ver = TRUE)
Arguments
query |
Character vector of length 1; query string to search GenBank. |
strict |
Logical vector of length 1; should an error be issued if the number of unique accessions retrieved does not match the number of hits from GenBank? Default TRUE. |
drop_ver |
Logical vector of length 1; should the version part of the accession number (e.g., '.1' in 'AB001538.1') be dropped? Default TRUE. |
Details
Note this queries NCBI GenBank, not the local database generated with restez.
It can be used either to restrict the accessions used to construct the local
database (acc_filter argument of db_create()) or to specify accessions
to read from the local database (id argument of gb_fasta_get() and other
gb_*_get() functions).
Value
Character vector; accession numbers resulting from query.
See Also
Examples
## Not run:
# requires an internet connection
cmin_accs <- ncbi_acc_get("Crepidomanes minutum")
length(cmin_accs)
head(cmin_accs)
## End(Not run)
Print file size predictions to screen
Description
Predicts the file sizes of the downloads and the database from the GenBank filesize information. Conversion factors are based on previous restez downloads.
Usage
predict_datasizes(uncompressed_filesize)
Arguments
uncompressed_filesize |
GBs of the stated filesize, numeric |
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Print method for status class
Description
Prints to screen the three sections of the status class. Not meant to be used interactively.
Usage
## S3 method for class 'status'
print(x, ...)
Arguments
x |
Status object |
... |
Other arguments (not used by this function) |
Create README in restez_path
Description
Write notes for the curious sorts who peruse the restez_path.
Usage
readme_log()
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Example GenBank record
Description
Example GenBank record in text format for demonstration purposes.
Usage
data("record")Format
A large character object containing record information and DNA sequence.
Source
https://www.ncbi.nlm.nih.gov/nuccore/AY952423.1
References
GenBank
Examples
data(record)
cat(record)
Connect to the restez database
Description
Sets a connection to the local database.
Usage
restez_connect(read_only = FALSE)
Arguments
read_only |
Logical; should the connection be made in read-only mode? Read-only mode is required for multiple R processes to access the database simultaneously. Default FALSE. |
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Disconnect from restez database
Description
Safely disconnect from the restez connection
Usage
restez_disconnect()
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Check restez filepath
Description
Raises error if restez path does not exist.
Usage
restez_path_check()
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Get restez path
Description
Return filepath to where the restez database is stored.
Usage
restez_path_get()
Value
character
See Also
Other setup:
restez_path_set(),
restez_path_unset(),
restez_ready(),
restez_status()
Examples
library(restez)
# set a restez path with a tempdir
restez_path_set(filepath = tempdir())
# check what the set path is
(restez_path_get())
Set restez path
Description
Specify the filepath for the local GenBank database.
Usage
restez_path_set(filepath)
Arguments
filepath |
character, valid filepath to the folder where the database should be stored. |
Details
Adds 'restez_path' to options(). In this path the folder 'restez' will be created and all downloaded and database files will be stored there.
See Also
Other setup:
restez_path_get(),
restez_path_unset(),
restez_ready(),
restez_status()
Examples
## Not run:
library(restez)
restez_path_set(filepath = 'path/to/where/you/want/files/to/download')
## End(Not run)
Unset restez path
Description
Set the restez path to NULL
Usage
restez_path_unset()
See Also
Other setup:
restez_path_get(),
restez_path_set(),
restez_ready(),
restez_status()
Is restez ready?
Description
Returns TRUE if a restez SQL database is available. Use restez_status() for more information.
Usage
restez_ready()
Value
Logical
See Also
Other setup:
restez_path_get(),
restez_path_set(),
restez_path_unset(),
restez_status()
Examples
library(restez)
fp <- tempdir()
restez_path_set(filepath = fp)
demo_db_create(n = 5)
(restez_ready())
db_delete(everything = TRUE)
(restez_ready())
Restez readline
Description
Wrapper for base readline.
Usage
restez_rl(prompt)
Arguments
prompt |
character, display text |
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Check restez status
Description
Report to console current setup status of restez.
Usage
restez_status(gb_check = FALSE)
Arguments
gb_check |
Check whether last download was from latest GenBank release? Default FALSE. |
Details
Set gb_check=TRUE to see if your downloads are up-to-date.
Value
Status class
See Also
Other setup:
restez_path_get(),
restez_path_set(),
restez_path_unset(),
restez_ready()
Examples
library(restez)
fp <- tempdir()
restez_path_set(filepath = fp)
demo_db_create(n = 5)
restez_status()
db_delete(everything = TRUE)
# Errors:
# restez_status()
Scan a gzipped file for text
Description
Scans a zipped file for text strings and returns TRUE if any are present.
Usage
search_gz(terms, path)
Arguments
terms |
Character vector; search terms (most likely GenBank accession numbers) |
path |
Path to the gzipped file to scan |
Value
Logical
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Log the system session information in restez path
Description
Records the session and system information to file.
Usage
seshinfo_log()
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Set up test common test data
Description
Creates temporary test folders.
Usage
setup()
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Retrieve GenBank selections made by user
Description
Returns the selections made by the user.
Usage
slctn_get()
Details
If no file found, returns empty character vector.
Value
character vector
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_log(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Log the GenBank selection made by a user
Description
This function is called whenever a user makes a selection with
the db_download(). It records GenBank numbers selections.
Usage
slctn_log(selection)
Arguments
selection |
selected GenBank sequences, named vector |
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
sql_path_get(),
stat(),
status_class(),
testdatadir_get()
Get SQL path
Description
Return path to where SQL database is stored.
Usage
sql_path_get()
Value
character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
stat(),
status_class(),
testdatadir_get()
Print blue
Description
Print to console blue text to indicate a number/statistic.
Usage
stat(...)
Arguments
... |
Any number of text arguments to print, character |
Value
coloured character encoding, character
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
status_class(),
testdatadir_get()
Generate a list class for storing status information
Description
Creates a three-part list for holding information on the status of the restez file path.
Usage
status_class()
Value
Status class
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
testdatadir_get()
Get test data directory
Description
Get the folder containing test data.
Usage
testdatadir_get()
See Also
Other private:
add_rcrd_log(),
cat_line(),
char(),
check_connection(),
cleanup(),
connected(),
connection_get(),
db_download_intern(),
db_sqlngths_get(),
db_sqlngths_log(),
dir_size(),
dwnld_path_get(),
dwnld_rcrd_log(),
entrez_fasta_get(),
entrez_gb_get(),
extract_accession(),
extract_by_patterns(),
extract_clean_sequence(),
extract_definition(),
extract_features(),
extract_inforecpart(),
extract_keywords(),
extract_locus(),
extract_organism(),
extract_seqrecpart(),
extract_sequence(),
extract_version(),
file_download(),
filename_log(),
flatfile_read(),
gb_build(),
gb_df_create(),
gb_df_generate(),
gb_sql_add(),
gb_sql_query(),
gbrelease_check(),
gbrelease_get(),
gbrelease_log(),
has_data(),
identify_downloadable_files(),
last_add_get(),
last_dwnld_get(),
last_entry_get(),
latest_genbank_release(),
latest_genbank_release_notes(),
message_missing(),
mock_def(),
mock_gb_df_generate(),
mock_org(),
mock_rec(),
mock_seq(),
predict_datasizes(),
readme_log(),
restez_connect(),
restez_disconnect(),
restez_path_check(),
restez_rl(),
search_gz(),
seshinfo_log(),
setup(),
slctn_get(),
slctn_log(),
sql_path_get(),
stat(),
status_class()