ensembl perlapi cannot get adaptor

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);

perl-api snp ensembl

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updated 10.2 years ago by Emily

• written 10.2 years ago by Viktor Bojovic •

1 answer

Have you installed the external dependancy "Tabix"? The use of the VCFCollection module does requires tabix. Please check our help on "Alleles and genotypes " and installation page for more details. Will's post is worthwhile a look too!

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written 10.2 years ago by Denise CS

i have tried to install it but i had problems.

root@splitbit:/usr/local/src/tabix-master/perl# perl Makefile.PL PREFIX=/usr/local/src/
Only one of PREFIX or INSTALL_BASE can be given.  Not both.
root@splitbit:/usr/local/src/tabix-master/perl# make
root@splitbit:/usr/local/src/tabix-master/perl# make install
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Appending installation info to /root/src//lib/x86_64-linux-gnu/perl/5.20.2/perllocal.pod 
root@splitbit:/usr/local/src/tabix-master/perl# ls
blib  Makefile  Makefile.PL  MANIFEST  MYMETA.json  MYMETA.yml  pm_to_blib  t  Tabix.bs  Tabix.c  TabixIterator.pm  Tabix.o  Tabix.pm  Tabix.xs  typemap
root@splitbit:/usr/local/src/tabix-master/perl# chmod 755 Tabix.o 
root@splitbit:/usr/local/src/tabix-master/perl# ./Tabix.o 
bash: ./Tabix.o: cannot execute binary file: Exec format error
root@splitbit:/usr/local/src/tabix-master/perl# file ./Tabix.o 
./Tabix.o: ELF 64-bit LSB relocatable, x86-64, version 1 (SYSV), not stripped

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written 10.2 years ago by Viktor Bojovic •

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.

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written 10.2 years ago by Jean-Karim Heriche