Re^2: Problems with ensembl perl script

[bioinfo]

Thank you both for the help and for your time. I'm stuck with this problem and do not know how to fix it. I made this change that you propose tfrayner but still gives an error:

-------------------- EXCEPTION --------------------
MSG: [Bio::EnsEMBL::Compara::Member=HASH(0x9adfe40)] must be a Bio::En
+sEMBL::Compara::MethodLinkSpeciesSet object

STACK Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_Meth
+odLinkSpeciesSet_orthology_type_subtype /home/david/src/ensembl-compa
+ra/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm:430
STACK toplevel ortologos.pl:35
---------------------------------------------------

I started with perl and Ensembl recently and I do not quite understand yet. The documentation is here:

http://www.ensembl.org/info/docs/api/Pdoc/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.html#POD7

So there should show only the orthologous of Mammalia which are one-to-one.This another code works and returns all species homologues, but I only want mammalian orthologues.

use strict;
    use warnings;
    use Bio::EnsEMBL::Registry;
    ## Load the registry automatically
    my $reg = "Bio::EnsEMBL::Registry";
    $reg->load_registry_from_url('mysql://[e-mail].
+org');
    ## Get the human gene adaptor
    my $human_gene_adaptor =
        $reg->get_adaptor("Homo sapiens", "core", "Gene");
    ## Get the compara member adaptor
    my $member_adaptor =
        $reg->get_adaptor("Compara", "compara", "Member");
    ## Get the compara homology adaptor
    my $homology_adaptor =
        $reg->get_adaptor("Compara", "compara", "Homology");



    my @BreastCANgenes = ('ABCA3','ABCB10','ABCB8','ACADM');

    open ("archivo", ">homologos.txt");
    my $gen;

    foreach $gen (@BreastCANgenes) {


    ## Get all existing gene object
    my $ctdp1_genes = $human_gene_adaptor->fetch_all_by_external_name(
+$gen);
    ## For each of these genes...
    foreach my $ctdp1_gene (@$ctdp1_genes) {
      ## Get the compara member
      my $member = $member_adaptor->fetch_by_source_stable_id(
          "ENSEMBLGENE", $ctdp1_gene->stable_id);
      ## Get all the homologues
      my $all_homologies = $homology_adaptor->fetch_all_by_Member($mem
+ber);
      ## For each homology
      foreach my $this_homology (@$all_homologies) {
        ## print the description (type of homology) and the
        ## subtype (taxonomy level of the event: duplic. or speciation
+)
        print $this_homology->description, " [", $this_homology->subty
+pe, "]\n";
        print archivo $this_homology->description, " [", $this_homolog
+y->subtype, "]\n";
        ## print the members in this homology
        my $members = $this_homology->get_all_Members();
        foreach my $this_member (@$members) {
          print archivo $this_member->source_name, " ",
        $this_member->stable_id, " (",
        $this_member->genome_db->name, ")\n"


        }
        print "\n";
      }
    }
    }
    close ("archivo");