Buenos días hermanos:
I need some help for this script:
use strict;
use warnings;
use Bio::EnsEMBL::Registry;
## Load the registry automatically
my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_url('mysql://anonymous@ensembldb.ensembl.
+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 ('Multi', 'compara', 'MethodLinkSpeciesSet')
+;
my @BreastCANgenes = ('ABCA3','ABCB10','ABCB8');
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 orthologues
my $all_homologies = $homology_adaptor->fetch_all_by_MethodLinkS
+peciesSet_orthology_type_subtype($member,'ortholog_one2one','Mammalia
+');
## 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');
it isn't works.
The error:
Can't locate object method "fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype" via package "Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor" at ortologos.pl line 34.
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