A few weeks ago, we released MyGene.info v3 API, which brings changes to exon field data structure and added accession version numbers to refseq and accession fields, along with some other back-compatible changes.
The mygene module itself has no incompatible changes (see detailed CHANGES.txt if you like). But you might want to check out the changes in our underlying v3 API from this detailed migration guide, especially if you are using refseq, accession and exon fields in your application.We encourage all of our users to upgrade to this new version. The upgrade is as easy as one line of command:
pip install mygene -U
To verify you have the latest version installed:
In : import mygene In : mygene.__version__ Out: '3.0.0'
And you can see it’s using our v3 API as the default now:
In : mg = mygene.MyGeneInfo() In : mg.url Out: 'http://mygene.info/v3'
As a side note, in case you still want to use our v2 URL for a while, you can still do that by setting
mg.url='http://mygene.info/v2'. Our v2 API will still be live till most of our users are migrated to v3 API, but the annotation data from v2 API will not be updated any more.
As always, you can find more info about our MyGene.info Python client here: