[ensembl-dev] Can't call method "genome_db" when use Ensembl_79

[Matthieu Muffato]

Right. Can you check the content of %zf_genes ? It probably contains undef

Matthieu

On 19/03/15 14:39, Liu Jialin wrote:
> Sure, thanks a lot. This part of script as below:
> 298   # if both speciation tests were ok, and there is only 1 zebrafish gene in each clupeocephala group
> 299   if (scalar(keys %zf_genes) eq 2) {
> 300     if ((scalar(@{$zf_genes{'1'}}) eq 1) and (scalar(@{$zf_genes{'2'}}) eq 1)) {
> 301       # check mouse orthologs: should have only 1
> 302       my @homologies;
> 303       foreach my $homology (@{$homology_adaptor >fetch_all_by_Member_paired_species(${$zf_genes{'1'}}[0], "Mus_musculus")}) {
> 304         if (($homology->taxonomy_level() eq 'Euteleostomi') and ($homology->description eq 'ortholog_one2many') and ($homology->is_tree_compliant() eq 1))     {
> 305           push(@homologies, $homology);
> 306         }
> 307       }
> 308       if (scalar(@homologies eq 1)){
> 309         print "\tThis tree was selected (mouse 3R dup orth STRICT)\n";
> 310         foreach my $member (@{$homologies[0]->gene_list}) {
> 311           if ($member->stable_id =~m/ENSMUSG/) {
> 312             open(OUT, '>>mouse_3Rdup_strict_orth.out') or die "Can't open file";
> 313             print OUT $member->stable_id, "\t", $root->tree->stable_id, "\t", $root->node_id, "\t", ${$zf_genes{'1'}}[0]->stable_id, "\t", ${$zf_genes{'2'    }}[0]->stable_id, "\n";
> 314             close OUT;
> 315           }
> 316         }
> 317       }
> 318     }
> 319   }
> 320   return;
> 321 }
> 322
>
> Cheers,
> Jialin
>
> ________________________________________
> From: dev-bounces at ensembl.org <dev-bounces at ensembl.org> on behalf of Matthieu Muffato <muffato at ebi.ac.uk>
> Sent: Thursday, March 19, 2015 3:25 PM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Can't call method "genome_db" when use Ensembl_79
>
> Hi Jialin,
>
> It looks like you are calling fetch_all_by_Member_paired_species() and
> the "member" object you are giving to the function is actually not defined.
> The problem thus happens before calling the function. Perhaps the gene
> you were expecting to find is not there any more ? or its name has changed ?
>
> Can you share that part of the script ?
>
> Matthieu
>
> On 19/03/15 14:19, Liu Jialin wrote:
>> Dear Ensemble team:
>>
>>
>> After ten minutes when I start run my script to query duplicates using
>> Ensembl_79, the system report a mistake:
>>
>> Can't call method "genome_db" on an undefined value at
>> /software/Development/Ensembl_API/79/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm
>> line 123.
>>
>>
>> However, when I use Ensembl_78, the script run normally, no such error
>> report.
>>
>> Any suggestion?
>>
>>
>> Jialin
>>
>
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-- 
Matthieu Muffato, Ph.D.
Ensembl Compara Project Leader
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
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