[ensembl-dev] Homology

[Javier Herrero]

Hi James

This error is typical when you fail to connect to the database.

I suspect you are using the HEAD code instead of the branch 64. The head 
code is already configured for connecting to the forthcoming database. 
Please switch your code to the 64 branch and try again:

cvs up -r branch-ensembl-64

Regards

Javier

On 11/11/11 19:29, Jan Vogel wrote:
> Hi James,
>
> the first script from the powerpoint works for me w/o problems or 
> modifications. I've tried schema 62 and schema 64 API's.
>
>
> The second one ( 'from the list' ) had some minor problems. It works 
> like this :
>
> my $member = 
> $member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE','ENSG00000004059');
>
> or
>
> my $member = 
> $member_adaptor->fetch_by_source_stable_id(undef,'ENSG00000004059');
>
> I did not try the zfish protein.
>
> Hth,
>    Jan
>
> On Nov 11, 2011, at 9:50 AM, James Blackshaw 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 <http://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 <http://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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>
>
>
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-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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