Creating a Local pyani
Database¶
pyani
stores genome information and analysis results in a persistent local SQLite3 database. This allows for reuse of previous comparisons and reanalysis of datasets without having to rerun the analysis. It also means that the genome comparison results don’t have to be stored in full on disk, saving space.
Note
To conduct a pyani
analysis, there needs to be an existing database in-place.
To create a new, empty database you can use the pyani createdb
command.
For more information about the pyani createdb
subcommand, please see the pyani createdb page, or issue the command pyani download -h
to see the inline help.
Create a new empty pyani
database¶
The basic form of the command is:
pyani createdb
This instructs pyani
to create a new, empty database for analysis at the default location.
Note
The default location for the pyani
database is in a hidden directory: .pyani/pyanidb
. All other pyani
subcommands will look in this location for the database, unless told otherwise using the --dbpath
option.
For example:
$ls .pyani
ls: .pyani: No such file or directory
$ pyani createdb
$ ls .pyani
pyanidb
Create an empty pyani
database at a specific location¶
Tip
If you use pyani
for a number of distinct taxa, it can be convenient to create a new database for each project, to avoid performance issues as the database grows in size, filled by data that does not contribute to the analysis.
The following command can be used to specify the location of the newly-created pyani
database:
pyani createdb --dbpath <PATH_TO_DATABASE>
where <PATH_TO_DATABASE>
is the intended location of the database. For instance, to create a new database specific for an analysis we’ll call multitaxa
, we could use the command:
$ ls .pyani
pyanidb
$ pyani createdb --dbpath .pyani/multitaxadb
$ ls .pyani
multitaxadb pyanidb
The new database can then be specified in other pyani
subcommands, using the --dbpath
option.