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

[Bhavana Harsha]

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_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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