[ensembl-dev] merging different compara masters

[Stephen Fitzgerald]

Hi Lel, as far as I know, we do not have such a script. You would have to 
do it manually or write your own script for this purpose. Apart from the 
genome_db table itself, six other tables in the compara schema have 
foreign key references to the genome_db_id field in the genome_db table.

dnafrag
gene_member
peptide_align_feature
seq_member
species_set
species_tree_node

In the lastz bds you would only need to change the entries in the 
genome_db, dnafrag and species_set tables before merging.

Cheers,
Stephen.


On Thu, 4 Sep 2014, Lel Eory wrote:

> Hello Compara-team,
>
> Can I merge two compara databases from different masters when the reference 
> genome is shared between the databases, but are represented with different 
> genome_db_ids?
> In my case I use a compara master DB to keep track of my pairwise alignments 
> and I use Ensembl core chicken (Galgal4 with genome_db_id=1) as a reference. 
> In Ensembl compara there is the 4 sauropsids EPO alignment which also has 
> Ensembl core chicken in it (Galgal4 with genome_db_id=142). The different 
> genome_db_ids break the consistency between the data-sets.
>
> Is there a script I can use which would merge the data-sets and would make 
> the reference genome_db_id consistent for the alignments (e.g. set the same 
> reference genome_db_id for the LastZ and EPO species_sets, dnafrags etc.), so 
> that I would be able to use the merged data to create the EPO_LOW_COVERAGE 
> alignment?
>
> Thank you.
>
> Best wishes,
> Lel
>
>
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