[ensembl-dev] API Perl Code Example Repository
Sumir Panji
sumir at sanbi.ac.za
Wed Feb 1 15:10:46 GMT 2012
Hello,
I am new to both PERL and using the Ensembl PERL API (version 65). I
have been looking around for any example PERL API scripts that I could
use to learn as well as adapt for my own use other then what is briefly
provided in the API tutorial docs. Is there a central repository that
contains sample code that can be used to figure out all the methods and
classes for the API? The one example I came across that I liked (taken
from slide 11 :
http://www.docstoc.com/docs/55683571/Ensembl-Developers-Workshop-Core-API)
does not seem to work very well.
#!/usr/bin/perl
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
my $gene_adaptor = $registry->get_adaptor('Human', 'Core', 'Gene');
my $genes-> fetch_all;
while (my $gene = shift @{$genes}){
print $gene->stable_id, "\n";
}
Error message : Can't call method "fetch_all" on an undefined value at
test_gene_ensembldb.pl line 14.
Thank you,
sumir
p.s I have been through all the mailing list archives 2006 - present
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