[ensembl-dev] Python Script to read emf dump files?

[Thomas Walsh]

Hello Omar,

My name is Thomas Walsh from the Ensembl Compara team, and I helped 
create the EMF files that you've expressed an interest in.

I understand that you're especially interested in accessing GERP and 
alignment data together. Is it necessary for this to be taken from an 
EMF file? Or are you primarily interested in loading the GERP and 
associated alignment data into Python, regardless of how it got there?

All the best,

Thomas Walsh.

> -------- Forwarded Message --------
> Subject: [ensembl-dev] Python Script to read emf dump files?
> Date: Thu, 2 Mar 2023 13:21:18 -0500
> From: Omar Gamel <omar.gamel at utoronto.ca>
> Reply-To: Ensembl developers list <dev at ensembl.org>
> To: dev at ensembl.org
> 
> Hello,
> 
> I am looking for a python package or script that can parse the 
> alignment emf files in the ENSEMBL FTP dump into an object I can 
> manipulate
> Example files here: 
> https://ftp.ensembl.org/pub/current_emf/ensembl-compara/multiple_alignments/90_mammals.epo_extended/
> I am particularly interested in the GERP data along with the alignment.
> 
> I see the example scripts provided are largely in perl: 
> https://github.com/Ensembl/ensembl-compara/tree/release/109/scripts/dumps
> 
> Please let me know where I can find such a python resource.
> 
> Thank you
> Omar

Thomas Walsh

Bioinformatics Developer, Ensembl Compara

European Bioinformatics Institute (EMBL-EBI)

Wellcome Genome Campus

Hinxton

Cambridge CB10 1SD

United Kingdom

Email: twalsh at ebi.ac.uk
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20230308/ce4ef393/attachment.html>