[Bioperl-l] (no subject)

Hermann Norpois hnorpois at googlemail.com
Tue Jun 5 17:10:13 EDT 2012


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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