[ensembl-dev] Problem with Compara

[Daniel Murphy]

Hi there,

I have a slight problem with a script I've written to find orthologs for a
list of mouse genes using the Ensembl Compara database. I have a large list
of genes and whenever I run the script I get an error message at some point
saying:

Can't call method "isa" on an undefined value at
/Network/.../Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm
line 185

When I remove the offending gene id from the list I'll get the error again
because of some other gene. This has happened to me before because of genes
no longer being in a new version of EnsEMBL, in this case however the genes
are in the latest EnsEMBL version but they aren't in the compara database,
perhaps because some of them may be predicted. The problem is whenever the
script comes across one of these genes the program exits instead of just
ignoring the gene and going to the next one. Rather than going through my
entire list of genes and manually removing any that aren't in the compara
database I'd like to just be able to skip any of the genes that aren't
found, so rather than the program exiting once it comes across a gene that
isn't in the database I'd like it to just continue with the next gene.
Is there any way to go about this? I appreciate any suggestions you might
have.

Regards,

Daniel Murphy
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