[ensembl-dev] Homology
James Blackshaw
jab250 at mrc-mbu.cam.ac.uk
Mon Nov 14 13:28:56 GMT 2011
I am definitely using v64 then, it's returned that.
-James
On 14/11/2011 12:56, Andy Yates wrote:
> You can run the following command (assuming the Ensembl API is on your PERL5LIB)
>
> perl -MBio::EnsEMBL::ApiVersion -e 'warn software_version()'
>
> Andy
>
> On 14 Nov 2011, at 12:51, James Blackshaw wrote:
>
>> Hi,
>> this still doesn't work, I get the error:
>> "Can't call method "fetch_by_source_stable_id" on an undefined value at homology_workshop_getAllHomologuesForGene.pl line 28."
>>
>> I get the following error off the script for comparing all homologs between two species. A pity, as that is otherwise perfect for what I want.
>> "Can't call method "get_HomologyAdaptor" on an undefined value at homology_getAllHomologuesBetween2Species.pl line 24."
>>
>> Is there anywhere I'd be able to check the version number of the API I have?
>>
>> Regards,
>> -James
>>
>> On 14/11/2011 12:02, Matthieu Muffato wrote:
>>> Hi James
>>>
>>> I just hope there is no misunderstanding with the line numbers. Your script seems to work well, at least here, replacing the $homology_adaptor->fetch_all_by_Member($member) line by $homology_adaptor->fetch_all_by_Member($member->gene_member)
>>>
>>> I can have the "dbID" error message when applying both changes. They are actually not compatible. Either you specify the gene ID in the first place, and stick with $homology_adaptor->fetch_all_by_Member($member), or you keep the protein ID, and you add the "->gene_member"
>>>
>>> There is a script in the scripts/examples directory of the ensembl-compara repository, named homology_workshop_getAllHomologuesForGene.pl, that does the job if you know the gene name.
>>>
>>> Regards,
>>> Matthieu
>>>
>>> On 14/11/11 11:41, James Blackshaw wrote:
>>>> Hi Matthieu,
>>>> Changing Line 16 doesn't help, I get the same error reported.
>>>> Changing line 25 gives me a new error though.
>>>> Can't call method "dbID" on an undefined value at
>>>> /usr/mbu/software/ensembl/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm
>>>> line 37.
>>>>
>>>> What I'm trying to do is get the homologs for a list of proteins or
>>>> associated genes, either works. I'm surprised there's not already a
>>>> script about for it, but can't find on on the mailing list.
>>>>
>>>> -James
>>>>
>>>>
>>>> On 14/11/2011 11:25, Matthieu Muffato wrote:
>>>>> Hi James
>>>>>
>>>>> In Comparam the homologies are stored at the gene level. Because your
>>>>> Member object represents a peptide, the homology list that you
>>>>> retrieve is empty.
>>>>>
>>>>> You can either change the line 25 to
>>>>> my $homologies =
>>>>> $homology_adaptor->fetch_all_by_Member($member->gene_member);
>>>>>
>>>>> or change the line 16 to
>>>>> my $member = $member_adaptor->fetch_by_source_stable_id("ENSEMBLGENE",
>>>>> ****) with an Ensembl gene ID if you know it
>>>>>
>>>>> to have all the homologies of your favourite gene
>>>>>
>>>>> Hope this helps,
>>>>> Matthieu
>>>>>
>>>>> On 14/11/11 11:15, James Blackshaw wrote:
>>>>>> Hi,
>>>>>> I am using the code from the API installation page and that page talks
>>>>>> about version 64.
>>>>>> http://www.ensembl.org/info/docs/api/api_installation.html
>>>>>>
>>>>>> This is my output under verbose, looks like it is connecting.
>>>>>> Odd number of elements in hash assignment at
>>>>>> /usr/mbu/software/ensembl/ensembl/modules/Bio/EnsEMBL/Utils/Argument.pm
>>>>>> line 148.
>>>>>> Transcript:ENSDART00000112153 Gene:ENSDARG00000090113 Chr:19
>>>>>> Start:33519855 End:33522332
>>>>>> Can't call method "get_all_Member_Attribute" on an undefined value at
>>>>>> sandbox3.pl line 47.
>>>>>>
>>>>>> Regards,
>>>>>> James
>>>>>>
>>>>>>
>>>>>> On 11/11/2011 20:20, Javier Herrero wrote:
>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Dev mailing list Dev at ensembl.org<mailto:Dev at ensembl.org>
>>>>>>>>> List admin (including subscribe/unsubscribe):
>>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Dev mailing listDev at ensembl.org<mailto:Dev at ensembl.org>
>>>>>>>> List admin (including
>>>>>>>> subscribe/unsubscribe):http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>> Ensembl Blog:http://www.ensembl.info/
>>>>>>> --
>>>>>>> Javier Herrero, PhD
>>>>>>> Ensembl Compara Project Leader
>>>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>>>> Wellcome Trust Genome Campus, Hinxton
>>>>>>> Cambridge - CB10 1SD - UK
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Dev mailing listDev at ensembl.org<mailto:Dev at ensembl.org>
>>>>>>> List admin (including
>>>>>>> subscribe/unsubscribe):http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>> Ensembl Blog:http://www.ensembl.info/
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>
>>>
>>
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> ---
> Andrew Yates Ensembl Core Software Project Leader
> EMBL-EBI Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK http://www.ensembl.org/
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