In this first tutorial we are going to build a database for all
rodents. The rodents are a good test case for playing with
restez as they are a relatively small domain in GenBank but
still have charismatic organisms that people are familiar enough with to
understand. We will also limit the number of sequences in the database
by limiting the sequence sizes between 100 and 1000.
The database you build here will be used again in later tutorials and
you may wish to experiment with it yourself. Therefore it is best to
locate a suitable place in your harddrive where you would like to store
it for later reference. In this tutorial and in others, we will always
refer to the rodents’ restez path with the variable
rodents_path.
Setting up the rodents database will likely take a long time. The exact time will depend on your internet speeds and machine specs. For reference, this vigenette was written on an iMac (2019) with a download speed of 56 MBPS. With this setup, downloading the database took 2.1 hr and creating the database took 7.4 hr.
Note GenBank domains (i.e., major parts of GenBank split by major
taxonomic group) are specified by number. As of writing, rodents are
number 7, but the numbering scheme may change between releases, so don’t
assume this will necessarily be the case in future releases. You can
check the current number scheme by running db_download()
without any input to preselection.
Download
library(restez)
# set the restez path to a memorable location
restez_path_set(rodents_path)
# download for domain 7 (rodents as of GenBank release 256)
db_download(preselection = '7')Build
db_create(min_length = 100, max_length = 1000)Check status
restez_status()
#> Checking setup status at ...
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Restez path ...
#> ... Path '[RODENTS PATH]/restez'
#> ... Does path exist? 'Yes'
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Download ...
#> ... Path '[RODENTS PATH]/restez/downloads'
#> ... Does path exist? 'Yes'
#> ... N. files 308
#> ... Total size 37.2G
#> ... GenBank division selections 'Rodent'
#> ... GenBank Release 256
#> ... Last updated '2023-07-23 08:43:34.776903'
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#> Database ...
#> ... Path '[RODENTS PATH]/restez/sql_db'
#> ... Does path exist? 'Yes'
#> ... Total size 845M
#> ... Does the database have data? 'Yes'
#> ... Number of sequences 263402
#> ... Min. sequence length 100
#> ... Max. sequence length 1000
#> ... Last_updated '2023-07-23 15:35:11.578151'