Accounts and Species¶

Accounts¶

You need to specify the host name (the domain name where there’s a running MySQL server hosting the Ensembl databases), username and password. Use the HostAccount class for this

>>> from ensembldb3 import HostAccount
>>> account = HostAccount("mysqlhostname.anu.edu.au", "username", "password")

You can also specify the port number, e.g. HostAccount(..., port=5306) if it differs from the default 3306.

I find it convenient to specify the MySQL server account details as an environment variable called ENSEMBL_ACCOUNT by adding the following to my .bashrc:

export ENSEMBL_ACCOUNT="mysqlhostname.anu.edu.au username password"

In my scripts I then create the HostAccount instance as

>>> import os
>>> from ensembldb3 import HostAccount
>>> account = HostAccount(*os.environ['ENSEMBL_ACCOUNT'].split())

Note

ensembldb3 defaults to using the Ensembl UK MySQL servers if you don’t specify an account.

Species¶

The Species class is a top level import that is used to translate between latin names and Ensembl’s database naming scheme. It also serves to allow the user to use just a species common name to reference it’s genome databases. The queries are case-insensitive.

>>> from ensembldb3 import Species
>>> print(Species)
=========================================================================================================
             Common name                Species name           Ensembl Db Prefix                Synonymns
---------------------------------------------------------------------------------------------------------
                  Alpaca               Vicugna pacos               vicugna_pacos
            Amazon molly            Poecilia formosa            poecilia_formosa
            Anole Lizard         Anolis carolinensis         anolis_carolinensis                         ...

You can directly extend the list of species, or modify an existing entry, using Species.amend_species. If you wish to edit the species list on a larger scale or just do it once so all your scripts can rely on that change, you can directly modify the reference species data used by ensembldb3.

See ensembldb3 exportrc to obtain the species data distributed with ensembldb3 plus other configuration files and edit the species.tsv file
Add an environment variable ENSEMBLDBRC to your .bashrc as follows:
```
export ENSEMBLDBRC="~/path/to/ensembldbrc/"
```

Note

The species.tsv file has at least 2, and up to 3, fields per line: species name, common name, species name synonym.

Look up a species common name¶

This can be done using the species name. Note that some synonyms are supported.

>>> Species.get_common_name("Felis catus")
'Cat'
>>> Species.get_common_name("Canis familiaris")
'Dog'
>>> Species.get_common_name("Canis lupus familiaris")
'Dog'