[ensembl-dev] Getting import_vcf.pl working

[Will McLaren]

Hello,

I'd recommend that you use the registry file rather than specifying the
connection parameters on the command line.

The problem with your registry file is that it does not return a true
value; all registry files must end with:

1;

as it is interpreted as a Perl module, and all Perl modules must return a
true value.

The DBAadaptor your file is creating should also be a Variation DBAdaptor,
and must have the species name specified in it.

Depending on your use case, you may also need to connect to a core
database; this should be specified as a non-variation DBAdaptor, as you had
before, but it should also have the species name included.

So, your registry file should look like:

use strict;

use Bio::EnsEMBL::Utils::ConfigRegistry;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;

new Bio::EnsEMBL::DBSQL::DBAdaptor(
  -species => 'Homo_sapiens',
  -user    => 'atchourb',
  -pass => 'abcd1234',
  -host    => 'localhost',
  -port    => '3306',
  -dbname  => 'my_core_database'
);

new Bio::EnsEMBL::Variation::DBSQL::DBAdaptor(
  -species => 'Homo_sapiens',
  -user    => 'atchourb',
  -pass => 'abcd1234',
  -host    => 'localhost',
  -port    => '3306',
  -dbname  => 'VCFdump'
);

my @aliases = ( 'H_Sapiens', 'human' );

Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
  -species => 'Homo sapiens',
  -alias   => \@aliases
);

1;

There's a slightly better example of a registry file (with the main
ensembldb parameters entered) here:

http://www.ensembl.org/info/docs/variation/vep/vep_script.html#local

Hope this helps!

Will McLaren
Ensembl Variation


On 22 February 2013 23:52, Tchourbanov, Alexander Y - (atchourb) <
atchourb at email.arizona.edu> wrote:

>  Dear ENSEMBL developers,
>
>  When I try to download VCF file to the locally installed database using
> the following command:
>
>  perl ./import_vcf.pl -i ./common_all.vcf.gz -db VCFdump -u atchourb
> --password abcd1234 --source dbSNP --population general
>
>  I get the following message:
>
>  Use of qw(...) as parentheses is deprecated at
> /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1564.
> 2013-02-22 16:33:54 - Session ID is a9703281edc05675ba906f396b0586fb
> human is not a valid species name for this instance
> Use of uninitialized value $species in hash element at
> /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 958.
> Use of uninitialized value $species in hash element at
> /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 969.
> ERROR: Could not get population adaptor
>
>  What is the way to get the population adapter? Are there more detailed
> instructions on how to download de novo VCF file to a database with
> import_vcf.pl?
>
>  Another question refers to usage of the registry file, which I never
> managed to get working:
>
>  use strict;
>
>  use Bio::EnsEMBL::Utils::ConfigRegistry;
> use Bio::EnsEMBL::DBSQL::DBAdaptor;
> use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
>
>  new Bio::EnsEMBL::DBSQL::DBAdaptor(
>   -user    => 'atchourb',
>   -pass => 'abcd1234',
>   -host    => 'localhost',
>   -port    => '3306',
>   -dbname  => 'VCFdump'
> );
>
>  my @aliases = ( 'H_Sapiens', 'human' );
>
>  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
>   -species => 'Homo sapiens',
>   -alias   => \@aliases
> );
>
>  after running the program I get the following message:
>
>  Use of qw(...) as parentheses is deprecated at
> /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1564.
> 2013-02-22 16:40:30 - Session ID is dd2fc7598559030f21bfcc9bc529162f
> ./registry.conf did not return a true value at
> /usr/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 360.
>
>  Thanks for any suggestions!
>
>
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