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arq5x / ggd

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How about GENCODE retreival #1

Open stephenturner opened 10 years ago

stephenturner commented 10 years ago

Data and links to FTP sites for human and mouse.

arq5x commented 10 years ago

Yep, good idea. I am currently looking into how best to pull data from Ensembl. Not that easy, unfortunately. Also, if you are interested in adding a recipe to ggd-recipes, that would be great!

martijnvermaat commented 10 years ago

Could have a look at how https://github.com/hammerlab/pyensembl rolls.

arq5x commented 10 years ago

Ah, thanks. Will have a look.

arq5x commented 10 years ago

By my eye, it appears that pyensembl rolls by creating a local instance of a SQLite database by downloading the relevant gzipped GTF, etc. files from Ensembl. This strategy could work, but ideally, I would really like GGD to use the existing APIs to pull data. This is going to be a challenge, however...

mw55309 commented 9 years ago

Aren't the Ensembl APIs in Perl?

arq5x commented 9 years ago

They have a MYSQL database under the hood as well.