[ensembl-dev] Variation Features from Slice

[Stuart Meacham]

Hi Will,

Thanks very much for the quick reply! And you're right, a sort of buglet 
. . . my loop was nested within one getting the gene_name

foreach my $go (@{$gene_adaptor->fetch_all_by_Slice($slice) }){
     [PREVIOUS SNP CODE]
}

However for some reason this wasn't retrieving a gene object thus the 
code was never invoked.

Cheers

Stuart

On 01/05/13 15:08, Will McLaren wrote:
> 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 <http://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 
> <mailto: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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