[Bioperl-l] (no subject)

Fields, Christopher J cjfields at illinois.edu
Tue Jun 5 17:20:15 EDT 2012


Hermann,

You may get an answer here, but for Ensemble-related questions you should post to the Ensembl mail list.  Ensembl uses very old (and no longer actively supported) version of BioPerl.

chris

On Jun 5, 2012, at 4:10 PM, Hermann Norpois wrote:

> Hello,
> 
> actually I wish to get ensembl transcript IDs for some gene names. For
> addressing this I tried some syntax ( to become more familiar with bioperl
> and ensembl) but it doesnt work even for easier things, for instance for
> getting DBEntries. So I guess there is a principal mistake in my script.
> Can anybody help me?
> 
> Thanks,
> Hermann Norpois
> 
> 
> 
> #!/bin/perl -w
> 
> use strict;
> 
> 
> use Bio::EnsEMBL::Registry;
> 
> 
>    my $registry = 'Bio::EnsEMBL::Registry';
> 
>    $registry->load_registry_from_db(
>        -host => 'ensembldb.ensembl.org', # alternatively '
> useastdb.ensembl.org'
>        -user => 'anonymous'
>    );
> 
>   #my $name = "Bdnf";
>    my $gene_adaptor = $registry -> get_adaptor( 'Mouse', 'Core', 'Gene');
>       my $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000184129');
>    #my $gene = $gene_adaptor -> fetch_all_by_external_name ($name);
>    my @dbentries = @{ $gene->get_all_DBEntries() };
>    my $info = join (":", @dbentries);
>    print "$info\n";
> #    print $gene -> seq(), "\n";
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