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

[Omar Gamel]

Hi Thomas,

Thank you for your response.
I am interested in loading the GERP and associated alignment data into
Python,  not necessarily from an EMF file.
Right now I loaded the human genome and gerp scores separately from release
109 FTP, matching them by position.
I would similarly like to be able to get the gerp for an entire alignment.

Best
Omar

On Wed, Mar 8, 2023 at 5:56 PM Thomas Walsh <twalsh at ebi.ac.uk> wrote:

> 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
>
>
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