[ensembl-dev] retrieve conservation score of all human exons

[Stephen Fitzgerald]

Hi Julien, if you are in Chicago you could try the useastdb.ensembl.org 
mirror, it may be faster for you.

my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_db(
  -host => "useastdb.ensembl.org",
  -port => 5306,
  -db_version => 74,
  -user => "anonymous",
);

Cheers,
Stephen.



On Thu, 16 Jan 2014, Julien Roux wrote:

> Dear list,
> I have been trying to extract the mean GERP conservation score for all human 
> exons using the Ensembl API.
> My script is working properly, however it is quite slow (only ~1000 exons per 
> hour) and I am wondering if there would be a way to speed it up.
> I have tried to set "display_size" to 1, but t doesn't seem to give yield the 
> exact mean score (because it is an average of precalculated averages I 
> guess).
> I am putting the script below.
> Thanks for your help
> Julien
>
> #!/usr/bin/env perl
> use strict;
> use warnings;
> use Bio::EnsEMBL::Registry;
> use Bio::EnsEMBL::Utils::Exception qw(throw);
>
> # This script is inspired by the example script at 
> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-compara/scripts/examples/dna_getConservationScores.pl?root=ensembl&view=markup
>
> my $reg = "Bio::EnsEMBL::Registry";
> my $species = "Homo sapiens";
> $reg->load_registry_from_db(
>       -host => "ensembldb.ensembl.org",
>       -user => "anonymous",
> );
>
> #get slice adaptor for $species
> my $slice_adaptor = $reg->get_adaptor($species, 'core', 'Slice');
>
> #get exon adaptor for $species
> my $exon_adaptor = $reg->get_adaptor($species, 'Core', 'Exon');
>
> #get method_link_species_set adaptor
> my $mlss_adaptor = $reg->get_adaptor("Multi", "compara", 
> "MethodLinkSpeciesSet");
>
> #get method_link_species_set object for gerp conservation scores for mammals
> my $mlss = 
> $mlss_adaptor->fetch_by_method_link_type_species_set_name("GERP_CONSERVATION_SCORE", 
> "mammals");
>
> #get conservation score adaptor
> my $cs_adaptor = $reg->get_adaptor("Multi", 'compara', 'ConservationScore');
>
> # fetch all exon IDs
> my @exon_ids = @{$exon_adaptor->list_stable_ids()};
>
> foreach my $exon (@exon_ids){
>   print $exon, "\n";
>   my $slice = $slice_adaptor->fetch_by_exon_stable_id($exon);
>
>   #get one score per base in the slice
>   my $display_size = $slice->end - $slice->start + 1;
>   my $scores = 
> $cs_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss, $slice, 
> $display_size);
>
>   # average the scores in the slice
>   my $sum = 0;
>   my $count = 0;
>   my $diff_score;
>   foreach my $score (@$scores) {
>     if (defined $score->diff_score) {
>       $sum += $score->diff_score;
>       $count++;
>     }
>   }
>   if ($count > 0){
>     $diff_score = $sum / $count;
>   }
>   if (defined $diff_score){
>     print "$exon\t$diff_score\n";
>   }
>   else {
>     print "$exon\tNA\n";
>  }
> }
> close OUT;
> exit;
>
> -- 
> Julien Roux, PhD
> Gilad lab, Department of Human Genetics, University of Chicago
> http://giladlab.uchicago.edu/
> 920 East 58th Street, CLSC 317, Chicago, IL 60637, USA
> tel: +1-773-834-1984   fax: +1-773-834-8470
>
>
> -- 
> Julien Roux, PhD
> Gilad lab, Department of Human Genetics, University of Chicago
> http://giladlab.uchicago.edu/
> 920 East 58th Street, CLSC 317, Chicago, IL 60637, USA
> tel: +1-773-834-1984   fax: +1-773-834-8470
>
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