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

[Bhavana Harsha]

Hi Matthieu,

Thanks for the clarification. I hadn't noticed that it should use 'gene_tree_root_id' instead.

Cheers,
Bhavana

> ------------------------------
> 
> Message: 3
> Date: Tue, 18 Feb 2014 23:31:25 +0000
> From: Matthieu Muffato <muffato at ebi.ac.uk>
> Subject: Re: [ensembl-dev] Possible bug in Ensembl Compara release 74
> 	-	HomologyAdaptor->fetch_all_by_tree_node_id()
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID: <5303ED4D.4030401 at ebi.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
> 
> 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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