[ensembl-dev] Problem with DumpAlignedGenes.pl script

[Harris, Ronald Alan]

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
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