[ensembl-dev] nsSNP difference between script and website

Will McLaren wm2 at ebi.ac.uk
Tue Nov 9 14:51:48 GMT 2010


Hi Tjaart,

Thanks for spotting this. The API code you have is fine; it is giving
you the correct set of non-synonymous variants.

Unfortunately there is a bug in this web display which means some
incorrect information is being shown. If you click on the "View" link
next to "Non-synonymous coding" on this page:

http://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?db=core;g=ENSG00000211772;r=7:142498725-142500432

you can see the same variants as your script is showing.

We will endeavor to get a patch for this bug in soon.

Thanks,

Will McLaren
Ensembl Variation


On 9 November 2010 14:07,  <tjaart at ebi.ac.uk> wrote:
> Hi guys
>
> I am trying to get the non_synonymous snps associated with a specific
> human transcript. Until version 59 of Ensembl the following script worked:
>
> #!/usr/bin/perl -w
> use strict;
> use warnings;
> use Bio::EnsEMBL::Registry;
> use Getopt::Long;
>
> my $registry = 'Bio::EnsEMBL::Registry';
>
> $registry->load_registry_from_db(
>    -host => 'ensembldb.ensembl.org',
>    -user => 'anonymous',
> );
>
> &GetOptions('trans:s' => \my $trans);
>
> my $stable_id =$trans;
> my $transcript_adaptor = $registry->get_adaptor('homo sapiens', 'core',
> 'transcript');
> my $transcript = $transcript_adaptor->fetch_by_stable_id($stable_id);
>
> my $trv_adaptor = $registry->get_adaptor('homo sapiens', 'variation',
> 'transcriptvariation');
> my $trvs = $trv_adaptor->fetch_all_by_Transcripts([$transcript]);
>
> foreach my $tv (@{$trvs})
> {
>        my $cons = join(",",@{$tv->consequence_type});
>        if ($cons =~ /NON_SYNONYMOUS_CODING/)
>        {
>                print $tv->translation_start()," ";
>                print $tv->pep_allele_string();
>                print "\n";
>        }
> }
>
> When running it this morning I get results that differ from the current
> Ensembl website.
>
> For transcript ENST00000466254 I get the following variants using my script:
>
> NON_SYNONYMOUS_CODING 37 Y/F rs1042956
> NON_SYNONYMOUS_CODING 104 S/L rs61732509
> NON_SYNONYMOUS_CODING 117 V/F rs56261425
>
> When looking at the webpage
> (http://www.ensembl.org/Homo_sapiens/Transcript/ProtVariations?db=core;g=ENSG00000211772;r=7:142498725-142500432;t=ENST00000466254)
> I get 9 nsSNPs, none of which correspond to my nsSNPs:
>
> 37      rs1042956       Non-synonymous  A/T     W       S, T
> 38      rs1042957       Non-synonymous  C/T     Y       P, L
> 57      rs61732510      Non-synonymous  C/T     Y       A, V
> 58      rs1042959       Non-synonymous  A/G     R       Q, R
> 60      rs1062612       Non-synonymous  G/A     R       H, R
> 80      rs60112268      Non-synonymous  A/C     M       C, *
> 104     rs61732509      Non-synonymous  C/T     Y       W, R
> 116     rs56261425      Non-synonymous  G/T     YK      P, L
> 160     rs1042966       Non-synonymous  C/T     Y       P, L
>
> The dbSNP ids are present in the page but the amino acid changes differ
> from what I get with my script.
>
> Am I making an error somewhere in my script? I did upgrade the API as well
> to the latest version (60).
>
> Hope you guys can help.
>
> Tjaart
>
>
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
>




More information about the Dev mailing list