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

[Liu Jialin]

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
>

_______________________________________________
Dev mailing list    Dev at ensembl.org
Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/