[ensembl-dev] Inquiry: Cafe.v3 Input

Magali mr6 at ebi.ac.uk
Tue Jul 30 09:12:03 BST 2013


Hi Mike,

Our live mirrors only hold the last two releases.
Giving we are on release 72, you will find 71 and 72 databases there,
but not 70, which is the db_version you specified for your registry.

As for the species, if you want to use cat data, you probably want to
replace the human gene_adaptor with a cat one.

    L33: my $human_gene_adaptor = $reg->get_adaptor("Homo
    sapiens", "core", "Gene");

with

    L33: my $cat_gene_adaptor = $reg->get_adaptor("Felis
    catus", "core", "Gene");



Hope that helps,
Magali


On 29/07/13 23:16, Mike Montague wrote:
> Hello, 
>
> I submitted the inquiry (below) to Miguel Pignatelli and he suggested
> that I forward the question to you. Upon looking at our error
> messages, he suspects we're having an issue connecting with the
> database or else it may be a general API issue. I've attached the
> script that we are attempting to use.
>
> Thank you for your assistance -
> Mike Montague
> ____________
>
>
> Michael J. Montague, Ph.D.
> Post-Doctoral Research Associate
> The Genome Institute, Washington University School of Medicine
> 4444 Forest Park Avenue, Campus Box 8501
> St. Louis, MO 63108
> T. 718.809.4093
>
> Hello Miguel,
>
> With the release of Cafe.v3, we intend to use your script to obtain
> data from Ensembl for input into Cafe. We are interested in
> gene expansion outliers for the cat lineage (ID 9685) relative
> to Carnivora (ID 33554).
>
> We made a copy of get_expansions.pl (attached below) and added line 10
> to call on the Ensembl API here at the Genome Institute. It seems to
> load fine (line 28).
>
>     L10: use lib '/gscmnt/sata206/techd/ensembl_api/v70/ensembl/modules';
>
>
> The human adapter loads fine (line 33) but we're wondering what it has
> to do with cat?
>
>     L33: my $human_gene_adaptor = $reg->get_adaptor("Homo
>     sapiens", "core", "Gene");
>
>
> The problem is with line 35, which returns nothing so it crashes in
> lines 38, 39 and 40.
>
>     L35: my $comparaDBA =
>     Bio::EnsEMBL::Registry->get_DBAdaptor('Multi', 'compara');
>     L38: my $gene_member_adaptor   = $comparaDBA->get_GeneMemberAdaptor;
>
>
> Error:
>
>
>     test_get_expansions.pl 9685 > cat_expansions.txt
>
>     Can't call method "get_GeneMemberAdaptor" on an undefined value at
>     /gscuser/mmontagu/bin/test_get_expansions.pl line 38.
>     cafe_output$ 
>
> or
>
>     perl ~/bin/test_get_expansions.pl 9685 > cat_expansions.txt
>
>     DBD::mysql::db selectall_arrayref failed: Can't read dir of '.'
>     (errno: 24) at
>     /gscmnt/sata206/techd/ensembl_api/v70/ensembl/modules/Bio/EnsEMBL/Registry.pm
>     line 1600.
>
>     -------------------- WARNING ----------------------
>     MSG: Homo sapiens is not a valid species name (check DB and API
>     version)
>     FILE: Bio/EnsEMBL/Registry.pm LINE: 1187
>     CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 972
>     Date (localtime)    = Wed Jul 24 14:14:00 2013
>     Ensembl API version = 70
>     ---------------------------------------------------
>
>     -------------------- EXCEPTION --------------------
>     MSG: Can not find internal name for species 'Homo sapiens'
>     STACK Bio::EnsEMBL::Registry::get_adaptor
>     /gscmnt/sata206/techd/ensembl_api/v70/ensembl/modules/Bio/EnsEMBL/Registry.pm:974
>     STACK toplevel /gscuser/mmontagu/bin/test_get_expansions.pl:33
>     Date (localtime)    = Wed Jul 24 14:14:00 2013
>     Ensembl API version = 70
>     ---------------------------------------------------
>
>
> Mainly, we were wondering if the inputs for lines 33 and 35 are
> correct for cat? 
>
>
> Or alternatively, are we calling on an incorrect version of the API?
> Or, perhaps were overlooking something else altogether?
>
>
>
>
>> *From: *mp at ebi.ac.uk <mailto:mp at ebi.ac.uk>
>> *Subject: **Re: Inquiry: Cafe.v3 Input*
>> *Date: *July 27, 2013 9:28:02 AM CDT
>> *To: *"Mike Montague" <mmontagu at genome.wustl.edu
>> <mailto:mmontagu at genome.wustl.edu>>
>> *Cc: *mp at ebi.ac.uk <mailto:mp at ebi.ac.uk>, "Wes Warren"
>> <wwarren at genome.wustl.edu <mailto:wwarren at genome.wustl.edu>>
>
>> Dear Mike,
>>
>> I am out of the office for some weeks with very limited access to the
>> internet at the moment. Looking at your error, it looks like the problem
>> is trying to connect with the DB or a general ensembl API problem. I
>> don't
>> have at hand the script, but if you can send the interesting parts to
>> ensembl-dev at ebi.ac.uk <mailto:ensembl-dev at ebi.ac.uk> you may be able
>> to find a useful answer in short
>> time.
>> I will take a look as soon as I can once I am back.
>>
>> Cheers,
>>
>> M;
>>
>>
>> *From: *Wes Warren <wwarren at genome.wustl.edu
>> <mailto:wwarren at genome.wustl.edu>>
>> *Subject: **Fwd: Re: Fwd: dN/dS*
>> *Date: *July 9, 2013 1:48:47 PM CDT
>> *To: *Mike Montague <mmontagu at genome.wustl.edu
>> <mailto:mmontagu at genome.wustl.edu>>
>>
>> Mike,
>>
>> The scripts you will need to retrieve cat data for cafe3. For cafe3
>> you need 1) a data file containing
>> gene family sizes for the taxa included in the tree and 2) a Newick
>> formatted tree, including branch lengths for each gene family. 
>>
>> Wes
>>
>> -------- Original Message -------
>> Subject: 	Re: Fwd: dN/dS
>> Date: 	Fri, 08 Mar 2013 17:24:06 +0000
>> From: 	Miguel Pignatelli <mp at ebi.ac.uk>
>> To: 	Wes Warren <wwarren at genome.wustl.edu>
>> CC: 	Javier Herrero <jherrero at ebi.ac.uk>, Matthieu
>> Muffato <muffato at ebi.ac.uk>
>>
>>
>>
>> Hi Wes,
>>
>> The CAFE data is stored in the compara database and is accessible via 
>> the compara API.
>>
>> I am sending you a file with the 43 genes expanded in cat with respect 
>> to the carnivora taxon.
>>
>> The columns in the file are:
>>
>> gene_tree_root_id, gene names, number of members in cat, number of 
>> members in the parent (carnivora), newick format of the species tree.
>>
>> A couple of comments about this data:
>>
>> - The newick tree contains the species names and the taxon_ids for the 
>> internal nodes. The numbers are the number of members for each taxon.
>> - I have only considered significant expansions as reported by our CAFE 
>> analysis. It would be possible to include genes in the "grey" zone (i.e. 
>> genes with more members in cat vs carnivora, but the change not being 
>> significant).
>>
>> I am also sending you the script I have written to retrieve the data. It 
>> accepts a taxon_id as input. I called it as follows:
>>
>> $ perl get_expansions.pl 9685 > cat_expansions.txt
>>
>> If you run the script with other taxon_ids, be aware that it also 
>> reports genes for which the lowest common ancestor is the taxon_id of 
>> interest (i.e. births at the taxon_id of interest).
>>
>> Let me know if you have any doubt or need further help in getting the 
>> data you want.
>>
>> Cheers,
>>
>> M;
>>
>>
>> On 07/03/13 20:15, Wes Warren wrote:
>> > Hi Miguel,
>> >
>> > Is this data available for cat? All the gene trees are available so I
>> > assume so but I am not sure where to find the CAFE files.
>> >
>> > Thanks,
>> > Wes
>> >
>> > On 3/7/13 12:15 PM, Javier Herrero wrote:
>> >> Hi Wes
>> >>
>> >> This is a question for Miguel, our CAFE expert.
>> >>
>> >> Javier
>> >>
>> >> On 06/03/13 17:00, Wes Warren wrote:
>> >>> Is the CAFE output available for cat? We are interested in gene
>> >>> expansion outliers for the cat lineage, perhaps correlating these
>> >>> with carnivora.
>> >>>
>> >>> Wes
>> >>>
>
>
>
>
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