[ensembl-dev] merging different compara masters

Lel Eory lel.eory at roslin.ed.ac.uk
Thu Sep 4 14:33:11 BST 2014


Thank you Stephen,
Lel

On 09/04/2014 01:22 PM, Stephen Fitzgerald wrote:
> 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
>>
>>
>> -- 
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
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