Entering edit mode
7.9 years ago
Viktor Bojovic
•
0
While trying to get adaptor using perlapi, i get undefined object, so im writting this to ask for help. my goal is to get frequency of genotypes and alleles for rs2242480, so im connecting to variation database. when i execute "$variation_adaptor->db->use_vcf(1);" i get: "Can't call method "db" on an undefined value"
use lib "/usr/local/src/ensembl/modules";
use strict;
use warnings;
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
my $variation_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'variation');
$variation_adaptor->db->use_vcf(1);
i have tried to install it but i had problems.
It seems you're trying to run an object file (tabix.o). These are usually intermediates in the compilation process and are not directly executable.