[ensembl-dev] error in homologyAdaptor.pm

[Javier Herrero]

Hi Koray

It seems you are using the fetch_all_by_Member method with an undefined object. 
If your code runs into that error, you should test whether the Member object 
is defined or not before using the fetch_all_by_Member method. If in a loop, 
something like this might help:

foreach my $stable_id (@all_stable_ids) {
  my $member = $member_adaptor->fetch_by_source_stable_id(
		"ENSEMBLGENE", $stable_id);
  if (!$member) {
    warn("No member with stable ID <$stable_id>");
    next;
  }
  my $homologies = $homology_adaptor->fetch_all_by_Member($member);
}

Javier

On Sunday 05 Dec 2010 09:06:04 Koray Doğan Kaya wrote:
> I got a list of fly genes,
> 
> I give this list to homology finding script
> 
> if the gene is hypothetical, script stops there
> 
> FBgn0037560
> Can't call method "dbID" on an undefined value at
> /home/koray/ensemblsrc/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/Ho
> mologyAdaptor.pm line 37, <RFILE> line 1.
> 
> how can i skip this...

-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK