[ensembl-dev] Fetching EPO multiple alignment

八號風球 panchengtsung at hotmail.com
Fri Jun 1 09:10:18 BST 2012

Dear all,

I used the DumpFakeMultiAlign.pl to try to fetch EPO MSA.
My first question is
How to set the registry_conf? or Can I set species in command without

I use "Bio::EnsEMBL::Registry->load_registry_from_url" to set my
Then run command
perl DumpFakeMultiAlign.pl --species human --seq_region 3
--seq_region_start 15112000 --seq_region_end 15113000 --alignment_type EPO

but encounter an error

------------------ DEPRECATED ---------------------
Deprecated method call in file DumpFakeMultiAlign.pl line 275.
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
STACK Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor::fetch_by_name_assembly
STACK toplevel DumpFakeMultiAlign.pl:278
Ensembl API version = 67

I tried to read manuals and Q&A, but it is not easy to understand for me so
Please give me some hints or solution.


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