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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)

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