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Hmm; I think I see what you're trying to do here, and I can see why you'd be frustrated. I've checked out the latest ensembl-compara code from CVS and it looks as though the (poorly named) fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype method has been removed, and it doesn't seem to have been replaced by anything with equivalent functionality. Maybe I'm wrong, and I guess the Ensembl devs would be the best people to ask. Maybe they've had a DB schema change that meant the old SQL query used to filter on subtype is no longer valid? Anyway, it may be that the best you can do is filter the homologies yourself:
## For each homology foreach my $this_homology (@$all_homologies) { next unless $this_homology->subtype eq 'Mammalia';
... and then the rest of your loop from the second script. That works on my machine and is reasonably fast, at least for this small gene set. I have no idea whether it will scale to meet your final requirements, though.

Cheers
Tim


In reply to Re^3: Problems with ensembl perl script by tfrayner
in thread Problems with ensembl perl script by bioinfo

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