[ensembl-dev] Update to homology TSV README on Ensembl FTP in release 116

[Thomas Walsh]

Hello,

For release 116, we are updating the README for homologies made 
available via Ensembl FTP in TSV format.

For Ensembl Vertebrates:

https://ftp.ebi.ac.uk/pub/ensembl/current_tsv/ensembl-compara/homologies/ 
[1]

For Ensembl Genomes (plants for example):

https://ftp.ebi.ac.uk/pub/ensemblgenomes/plants/current/tsv/ensembl-compara/homologies/ 
[2]

Among other things, the updated README clarifies the differences between 
the homology TSV files at the top level in the 'homologies' directory 
(each of which stores all available homologies for a given gene-tree 
collection) and the genome-specific homology TSV files within 
subdirectories named for a particular genome (each storing an arbitrary 
subset of homologies involving the given genome).

The way in which homologies are stored in genome-specific TSV files has 
implications for accessing them. To access all available orthologies 
between two or more genomes (e.g. 'drosophila_melanogaster' and 
'saccharomyces_cerevisiae'), you will need to download the 
genome-specific files of all relevant genomes (e.g. 
'drosophila_melanogaster/Compara.116.protein_default.homologies.tsv.gz' 
and 
'saccharomyces_cerevisiae/Compara.116.protein_default.homologies.tsv.gz').

An example script is available to illustrate how homologies in 
genome-specific TSV files may be accessed:

https://github.com/Ensembl/ensembl-compara/blob/release/116/scripts/examples/get_hom_tsv.py

This README will be included in Ensembl 116 release dumps, but you can 
already check out the README.gene_trees.tsv_dumps.txt file on GitHub:

https://raw.githubusercontent.com/Ensembl/ensembl-compara/refs/heads/release/116/docs/ftp/README.gene_trees.tsv_dumps.txt

All the best,

-- 

Thomas Walsh

Senior Bioinformatician, Ensembl Compara

European Bioinformatics Institute (EMBL-EBI)

Wellcome Genome Campus

Hinxton

Cambridge CB10 1SD

United Kingdom

Email: twalsh at ebi.ac.uk



Links:
------
[1] 
https://ftp.ebi.ac.uk/pub/ensembl/current_tsv/ensembl-compara/homologies/
[2] 
https://ftp.ebi.ac.uk/pub/ensemblgenomes/plants/current/tsv/ensembl-compara/homologies/
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