[ensembl-dev] Problem with DumpAlignedGenes.pl script

Kathryn Beal kbeal at ebi.ac.uk
Thu May 31 11:24:41 BST 2012


Hi Alan,
As you may have noticed, this script has not been updated for some time. I've made various updates and the script now works. I've committed this to the cvs ensembl-compara HEAD code. I'll send a separate email with this attached for you.

Cheers
Kathryn

> Hi,
>  
> I am trying to use the DumpAlignedGenes.pl in version 67 of the ensembl-compara API. I have made the following necessary changes to the script (attached script has these changes):
>  
> 1. When running the script without arguments as a test I get this error:
>  
> ------------------ DEPRECATED ---------------------
> Deprecated method call in file DumpAlignedGenes.pl line 365.
> Method Bio::EnsEMBL::DBSQL::MetaContainer::get_Species is deprecated.
> Call is deprecated. Use $self->get_common_name() / $self->get_classification() / $self->get_scientific_name() instead
> Ensembl API version = 67
> ---------------------------------------------------
> -------------------- EXCEPTION --------------------
> MSG: No matches found for name 'Homininae Homo sapiens' and assembly '--undef--'
> STACK Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor::fetch_by_name_assembly /home/rharris1/work/ensembl/api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm:131
> STACK toplevel DumpAlignedGenes.pl:369
> Ensembl API version = 67
>  
> I changed line 365 from
>  
> my $this_binomial_id = $this_meta_container_adaptor->get_Species->binomial;
>  
> to
>  
> my $this_binomial_id = $this_meta_container_adaptor->get_scientific_name;
> $this_binomial_id =~ s/\s/_/;
>  
> which fixes this error.
>  
> 2. I also get this similar error:
>  
> ------------------ DEPRECATED ---------------------
> Deprecated method call in file DumpAlignedGenes.pl line 436.
> Method Bio::EnsEMBL::DBSQL::MetaContainer::get_Species is deprecated.
> Call is deprecated. Use $self->get_common_name() / $self->get_classification() / $self->get_scientific_name() instead
> Ensembl API version = 67
> ---------------------------------------------------
> -------------------- EXCEPTION --------------------
> MSG: No matches found for name 'Murinae Rattus norvegicus' and assembly '--undef--'
> STACK Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor::fetch_by_name_assembly /home/rharris1/work/ensembl/api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm:131
> STACK toplevel DumpAlignedGenes.pl:440
> Ensembl API version = 67
> ---------------------------------------------------
>  
> I changed line 436 from
>  
> my $source_binomial_id = $meta_container_adaptor->get_scientific_name;
>  
> to
>  
> my $source_binomial_id = $meta_container_adaptor->get_scientific_name;
> $source_binomial_id =~ s/\s/_/;
>  
> which fixes this error.
>  
> ---------------------------------------------------------------------
>  
> Now I am getting this error:
>  
> Can't call method "get_all_Genes" on unblessed reference at DumpAlignedGenes.pl line 463.
>  
> Here is line 463:
>  
> my $mapped_genes = $align_slice->{'slices'}->{$source_genome_db->name}->get_all_Genes(
>  
> >>>How do I fix this error?<<<
>  
>  
> Thank you for your time.
>  
> Alan
>  
>  
> R. Alan Harris, Ph.D.
> Assistant Professor
> Bioinformatics Research Laboratory
> Epigenomics Data Analysis and Coordination Center
> Department of Molecular and Human Genetics
> Baylor College of Medicine
> Houston, TX 77030
> 713-798-7695
> <DumpAlignedGenes.pl>_______________________________________________
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