[ensembl-dev] Restricting species considered for ortholog requests

[Jason Merkin]

Hi Javier

Correct me if I am wrong but won't the paralog query give you the three
sets of genes in hsap? I would like to, for instance, get hsap1 without
getting hsap2, hsap2', or hsap3.

I wrote the following script to recursively get all homologies of all types
except paralog that I think should get and print out all of the members of
the gene family.

$stable = shift;

my %these_species;

foreach (9606, 10090){

        $these_species{$_} = 1;

}

my %relationships;

foreach ("ortholog_one2one", "ortholog_one2many", "ortholog_many2one",

        "ortholog_many2many", "possible_ortholog",
"apparent_ortholog_one2one"){

        $relationships{$_} = 1;

}


my $homology_adaptor = $reg->get_adaptor("Compara", "compara", "Homology");

my $member_adaptor = $reg->get_adaptor('Multi', 'compara', 'Member');

my %these_genes;

my %query_used;

single_gene($stable, \%relationships, \%these_species, $member_adaptor,
$homology_adaptor, \%query_used);

while ( my ($key, $value) = each(%these_genes) ) {

                print "$key => $value\n";

                            }


sub single_gene

{

        #($stable, %relationships, %these_species, $member_adaptor,
$homology_adaptor)

        my $this_stable = @_[0];

        if ($query_used{$this_stable}){

                return;

        }

        $query_used{$this_stable} = 1;


        my $member =
$member_adaptor->fetch_by_source_stable_id("ENSEMBLGENE", $this_stable);

        if (defined $member){

                my $all_homologies =
$homology_adaptor->fetch_by_Member($member);

                foreach my $homology (@{$all_homologies}) {

                        if ($relationships{$homology->description}){

                                foreach my $attr
(@{$homology->get_all_Member_Attribute}) {

                                        my ($member, $attribute) = @{$attr};

                                        if
($these_species{$member->taxon_id}){

                                                my $new_stable =
$member->stable_id;

                                                $these_genes{$new_stable} =
1;

                                                single_gene($new_stable,
\%relationships, \%these_species,

                                                        $member_adaptor,
$homology_adaptor, \%query_used);


                                        }

                                }

                        }

                }

        }

        return;

}

On Feb 13, 2012 6:48 AM, "Javier Herrero" <jherrero at ebi.ac.uk> wrote:

>  Hi Jason
>
> You can use the HomologyAdaptor (
> http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1HomologyAdaptor.html)
> to get these relationships. You can try either the
> fetch_all_by_Member_paired_species or the
> fetch_all_by_Member_paired_species methods. For instance,
>
> $homology_adaptor->fetch_all_by_Member_paired_species($hsap1_member,
> "mus_musculus", "ENSEMBL_ORTHOLOGUES");
>
> will return [$mmus1_member], and
>
> $homology_adaptor->fetch_all_by_Member_paired_species($hsap2_member,
> "mus_musculus", "ENSEMBL_ORTHOLOGUES");
>
> will return [$mmus2_member, $mmus2'_member]. If you want to get the
> intra-species paralogues as well, you can add:
>
> $homology_adaptor->fetch_all_by_Member_paired_species($hsap2_member,
> "homo_sapiens", "ENSEMBL_PARALOGUES");
>
> I hope this helps
>
> Javier
>
> On 12/02/12 01:24, Jason Merkin wrote:
>
> Hello. I am trying to identify duplications that have occured within a
> group of species. I have gone through the tutorial and the mailing list
> archives and couldn't find anything on it. I will use the example on the
> webpage that explains the homology definitions (
> http://ensembl.genomics.org.cn:8058/info/docs/compara/homology_method.html)
> to illustrate what I am trying to do. Using just human and mouse, as on the
> diagram, I would like to query with Hsap1 and get the set of (Hsap1,
> Mmus1); query with Hsap2 and get (Hsap2, Hsap2', Mmus2, Mmus2'); and query
> with Hsap3 and get (Hsap3, Mmus3, Mmus3'). Is there a way to specify the
> homology type and, more importantly, restrict the species to be considered
> for definining the homology?
>
> Thanks for any help,
> Jason Merkin
>
>
>
> _______________________________________________
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>
>
> --
> Javier Herrero, PhD
> Ensembl Coordinator and Ensembl Compara Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
>
>
> _______________________________________________
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> Ensembl Blog: http://www.ensembl.info/
>
>
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