[ensembl-dev] Variation Features from Slice

[Will McLaren]

Hi Stuart,

This works OK for me, both using this release's API (71) and the previous
(70).

Here's my script:

use strict;
use warnings;

use Bio::EnsEMBL::Registry;
my ($host, $port, $user, $pass, $species);

$host = 'ensembldb.ensembl.org';
$port = 5306;
$user = 'anonymous';
$pass = '';


my $reg = 'Bio::EnsEMBL::Registry';

$reg->load_registry_from_db(
        -host       => $host,
        -user       => $user,
        -pass       => $pass,
        -port       => $port,
);

my $sa = $reg->get_adaptor('homo_sapiens','core','slice');
my $vfa = $reg->get_adaptor('homo_sapiens','variation','variationfeature');

my $chr = '9';
my $pos = '136131022';
my $slice = $sa->fetch_by_region('chromosome',$chr,$pos,$pos); #create a
slice of 1 base length
    foreach my $vf (@{$vfa->fetch_all_by_Slice($slice)}){ #get all
variations at that position
        my $snp = $vf->variation_name();
        my $as = $vf->allele_string;
        my $maf = $vf->minor_allele_frequency();
        my $ma = $vf->minor_allele();
        my $cons = $vf->display_consequence();
        my $vc = $vf->var_class();
        print "$chr\t$pos\t$snp\t$as\t$cons\t$vc\n";
}

And the output:

9       136131022       rs8176751       C/T     downstream_gene_variant SNP

Perhaps you have a buglet somewhere in your script?

Regards

Will McLaren
Ensembl Variation


On 1 May 2013 14:50, Stuart Meacham <sm766 at cam.ac.uk> wrote:

> Hi,
>
> If I have the data chr:pos for a SNP can I expect to retrieve the
> Variation Feature(s) at that location via a Slice with something like:
>
> my $chr = '9';
> my $pos = '136131022'
> my $slice = $sa->fetch_by_region('**chromosome',$chr,$pos,$pos); #create
> a slice of 1 base length
>     foreach my $vf (@{$vfa->fetch_all_by_Slice($**slice)}){ #get all
> variations at that position
>         my $snp = $vf->variation_name();
>         my $as = $vf->allele_string;
>         my $maf = $vf->minor_allele_frequency();
>         my $ma = $vf->minor_allele();
>         my $cons = $vf->display_consequence();
>         my $vc = $vf->var_class();
>         print OUTPUT "$chr\t$pos\t$snp\t$as\t$cons\**t$vc\t$gene\n";
>     }
> }
>
> The reason I ask is because 9:136131022 doesn't seem to return rs8176751
> although I have had success with other locations.
>
> Thanks
>
> Stuart
>
>
>
>
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