[ensembl-dev] Homology

[Andy Yates]

Hi James,

Javier is quite right that this normally happens when you have used the wrong version of the Api. To see what the registry is loading you can add a 

-VERBOSE => 1

Argument to the load_registry_from_db() call.

Hope this helps,

Andy

P.S. if you downloaded the tar ball Api recently (about 1-2 weeks ago) then it had become corrupted but is ok now

Sent from my brain

On 11 Nov 2011, at 17:50, James Blackshaw <jab250 at mrc-mbu.cam.ac.uk> wrote:

> Hi,
> I've been trying to put together some scripts for finding the homolgies
> for some lists of genes I'm interested in, but I keep getting errors
> with the "fetch" methods.
> 
> "Can't call method "fetch_by_source_stable_id" on an undefined value at
> sandbox3.pl line 15."
> 
> I've used one script taken from a presentation by Stephen Fitzgerald at
> Edinburgh, and another from this maining list. I'm including both.
> 
> From the powerpoint:
> use strict;
> use Bio::EnsEMBL::Registry;
> my $reg = "Bio::EnsEMBL::Registry";
> 
> $reg->load_registry_from_db(
>    -host=>"ensembldb.ensembl.org",
>    -user =>  "anonymous");
> 
> 
> my $ma = $reg->get_adaptor(
>    "Multi", "compara", "Member");
> my $member = $ma->fetch_by_source_stable_id(
>    "ENSEMBLGENE", "ENSG00000000971");
> 
> my $homology_adaptor = $reg->get_adaptor(
>    "Multi", "compara", "Homology");
> 
> my $homologies = $homology_adaptor->
>    fetch_all_by_Member($member);
> 
> foreach my $this_homology (@$homologies) {
>  print $this_homology->description, "\n";
>  my $member_attributes = $this_homology->
>      get_all_Member_Attribute();
>  foreach my $this_mem_attr (@$member_attributes) {
>    my ($this_member, $this_attribute) =
>        @$this_mem_attr;
>    print $this_member->genome_db->name, " ",
>            $this_member->source_name, " ",
>            $this_member->stable_id, "\n";
>  }
>  print "\n";
> }
> 
> ==========================================
> 
> From the list:
> use Bio::EnsEMBL::Registry;
> Bio::EnsEMBL::Registry->load_registry_from_db(
>    -host =>  'ensembldb.ensembl.org',
>    -user =>  'anonymous',
>    -port =>  5306);
> my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
>    'Multi','compara','Member');
> 
> # fetch a Member
> # get the MemberAdaptor
> my $member_adaptor =
> Bio::EnsEMBL::Registry->get_adaptor('Multi','compara','Member');
> 
> # fetch a Memmy $member =
> $member_adaptor->fetch_by_source_stable_id('ENSEMBLPROTEIN','ENSG00000004059');
> my $member =
> $member_adaptor->fetch_by_source_stable_id('ENSEMBLPEP','ENSDARP00000103634');
> # print out some information about the Member
> print $member->description, "\n";
> 
> 
> 
> my $homology_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi',
> 'compara', 'Homology');
> my $homologies = $homology_adaptor->fetch_all_by_Member($member);
> 
> # That will return a reference to an array with all
> homologies(orthologues in
> # other species and paralogues in the same one)
> # Then for each homology, you can get all the Members implicated
> 
> foreach my $homology (@{$homologies}) {
>  # You will find different kind of description
>  # UBRH, MBRH, RHS, YoungParalogues
>  # see ensembl-compara/docs/docs/schema_doc.html for more details
> 
>  print $homology->description," ", $homology->subtype,"\n";
> # And if they are defined dN and dS related values
>  print " dn ", $homology->dn,"\n";
>  print " ds ", $homology->ds,"\n";
>  print " dnds_ratio ", $homology->dnds_ratio,"\n";
> }
> 
> my $homology = $homologies->[0];
> # take one of the homologies and lookinto it
> 
> foreach my $member_attribute (@{$homology->get_all_Member_Attribute}) {
> 
>  # for each Member, you get information on the Member specifically and in
>  # relation to the homology relation via Attribute object
> 
>  my ($member, $attribute) = @{$member_attribute};
>  print (join " ", map { $member->$_ }  qw(stable_id taxon_id))."\n";
>  print (join " ", map { $attribute->$_ } qw(perc_id
> perc_posperc_cov))."\n";
> 
> }
> ====================================================
> 
> 
> 
> James Blackshaw
> PhD Student
> MRC Mitochondrial Biology Unit
> 
> 
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