Beefy Boxes and Bandwidth Generously Provided by pair Networks
No such thing as a small change

Re: i need help to download text data from ensemble for a project

by erix (Vicar)
on Feb 28, 2012 at 13:45 UTC ( #956663=note: print w/replies, xml ) Need Help??

in reply to i need help to download text data from ensemble for a project

There is an extensive API for the ensembl data, but it's a bit of a learning curve.

Perhaps this is an easier way to get at their sixway primate alignment:

Main site -> links to -> links to There, the EMF link leads to: +/ (chromosome 11 is there, too)

The emf format is explained in a readme in that directory.

(if you prefer to get your stuff via the urls, make sure you give ample waiting times between the retrievals (i.e.: sleep 20, or whatever duration ensembl requests: it will be in their API's documentation ) or you risk being banned from ensembl servers.)

(BTW, it's EnsEMBL, without the -e. See EMBL)

Log In?

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://956663]
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others chilling in the Monastery: (7)
As of 2016-10-25 06:49 GMT
Find Nodes?
    Voting Booth?
    How many different varieties (color, size, etc) of socks do you have in your sock drawer?

    Results (315 votes). Check out past polls.