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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 http://www.ensembl.org/index.html -> links to http://www.ensembl.org/downloads.html -> links to http://www.ensembl.org/info/data/ftp/index.html There, the EMF link leads to: ftp://ftp.ensembl.org/pub/release-66/emf/ensembl-compara/epo_6_primate +/ (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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