[ensembl-dev] Possible bug in Ensembl Compara release 74 - HomologyAdaptor->fetch_all_by_tree_node_id()

Matthieu Muffato muffato at ebi.ac.uk
Tue Feb 18 23:31:25 GMT 2014


Dear Bhavana,

We've indeed spotted that bug recently and fixed the code for the 
upcoming version 75. I have now also backported the change to v74, so 
you should be able to pick it up with "git pull"

Best,
Matthieu

PS: The query should use *gene_tree_root_id*

On 18/02/14 16:49, Bhavana Harsha wrote:
> Hi,
>
> We have a custom Compara database for our 50 helminth genomes project,
> built by a bioinformatician in our team.
>
> I have been trying to get all homologies for a gene tree using the
> root_id of the tree, like so:
>
>
>     my $root_node_id = $gene_tree->root_id();
>     my $homologies =
>     $homology_adaptor->fetch_all_by_tree_node_id($root_node_id);
>
>
> This throws the following error:
>
>     -------------------- EXCEPTION --------------------
>     MSG: Detected an error whilst executing SQL 'SELECT h.homology_id,
>     h.method_link_species_set_id, h.description, h.is
>     <http://h.is/>_tree_compliant, h.dn, h.ds, h.n, h.s, h.lnl,
>     h.species_tree_node_id, h.gene_tree_node_id, h.gene_tree_root_id
>     FROM  (homology h)  WHERE  h.tree_node_id = ? ': DBD::mysql::st
>     execute failed: Unknown column 'h.tree_node_id' in 'where clause' at
>     /nfs/users/nfs_b/bh4/apps/ensembl-74/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm
>     line 168.
>
>     STACK Bio::EnsEMBL::Compara::DBSQL::BaseAdaptor::generic_fetch
>     /nfs/users/nfs_b/bh4/apps/ensembl-74/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm:170
>     STACK
>     Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_tree_node_id
>     /nfs/users/nfs_b/bh4/apps/ensembl-74/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm:255
>     STACK (eval) (eval 82)[/usr/share/perl/5.14/perl5db.pl:640]:2
>     STACK DB::eval /usr/share/perl/5.14/perl5db.pl:640
>     STACK DB::DB /usr/share/perl/5.14/perl5db.pl:3436
>     STACK main::get_all_one_to_one_orthologs
>     /nfs/users/nfs_b/bh4/git/helminth_scripts/scripts/get_fasta_for_one2one_orthologs_from_gene_trees_v74.pl:75
>     STACK toplevel
>     /nfs/users/nfs_b/bh4/git/helminth_scripts/scripts/get_fasta_for_one2one_orthologs_from_gene_trees_v74.pl:43
>     Date (localtime)    = Tue Feb 18 13:47:22 2014
>     Ensembl API version = 74
>     ---------------------------------------------------
>
>
> I can confirm that both our database and the API I'm using are version 74.
>
> The offending line is line 252
> in Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor.
> Turns out that there is no '*tree_node_id*' field in the homology table
> in the new release. Should this be '*h.gene_tree_node_id = ?*' instead?
>
> Regards,
> Bhavana
>
>
>
> ---------------------------------------------
> Bhavana Harsha
> Bioinformatician
> Parasite Genomics
> Wellcome Trust Sanger Institute
> Hinxton, UK
> CB10 1SA
>
>
>
>
>
>
>
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-- 
Matthieu Muffato, Ph.D.
Ensembl Developer and Ensembl Compara Manager
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468




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