[Bioperl-l] Ensembl problems

Albert Vilella avilella at gmail.com
Sun Jan 10 16:05:13 EST 2010

> However, if anyone knows Ensembl very well, the database has in it
> some of these interspecies comparisons already.  They are accessed
> when one does a phylogeny tree for specific genes (and generally for
> highly conserved gene you will get a tree that includes nearly all 50
> species in the database).  As I don't think they are computed
> on-the-fly, the information must be precomputed and stored someplace
> in the database.  I would very much like to know how to access this
> information.

Yes, they are. You can access the data programmatically by installing
the ensembl and ensembl-compara Perl APIs.
There are a few example scripts for the GeneTrees:




> Thanks,
> Robert
> On 1/9/10, Andreas Kähäri <ak at ebi.ac.uk> wrote:
>> On Sat, Jan 09, 2010 at 03:27:54PM -0500, Robert Bradbury wrote:
>>> I am trying to get the examples provided by EMBL/Ensembl to work and am
>>> encountering problems.
>> Hi Robert,
>> The ensembl-dev list is the appropriate forum for this type of questions
>> as it has nothing to do with bioperl.
>> There is also the Ensembl helpdesk.  If you send your problem to
>> <helpdesk at ensembl.org> I'm sure that it will be picked up by the
>> appropriate people (I do myself not know enough about the Compara API to
>> be able to diagnose this problem straight away I'm afraid).
>> Be sure to submit a minimal script that still exhibit the problem, and
>> information about what version of the APIs you're using (we will assume
>> that you're not mixing newer version of the API with older databases or
>> vice versa).
>> We are generally very happy to have bugs in documentation or code
>> pointed out to us, and will correct errors as we are made aware of them.
>> Kind regards,
>> Andreas
>>> For example, about 1/3 of the way through the Compara API tutorial [1]
>>> there
>>> is what is supposed to be a completely functional script.  It does not
>>> work.  This is in contrast to some of the earlier simple scripts (listing
>>> the species in  Ensmbl etc.) which do work on my machine, so I have all
>>> the
>>> libraries do dah installed correctly).
>>> Very poor form to document scripts which do not function on a properly
>>> setup
>>> system.
>>> I have modified my invocation of the script slightly:
>>>   Align.pl --set_of_species \
>>> "Homo sapiens:Pan troglodytes:Gorilla gorilla:Macaca mulatta:Otolemur
>>> garnettii:Pongo pygmaeus:Equus caballus:Bos taurus:Loxodonta
>>> africana:Pteropus vampyrus:Myotis lucifugus:Felis catus:Canis
>>> familiaris:Sus
>>> scrofa:Rattus norvegicus:Mus musculus:Gallus gallus:Xenopus
>>> tropicalis:Takifugu rubripes:Tetraodon nigroviridis:Danio rerio:Tupaia
>>> belangeri:Caenorhabditis elegans:Saccharomyces cerevisiae"
>>> which results in "Can't call method "fetch_by_method_link_type_GenomeDBs"
>>> on
>>> an undefined value at ./Align.pl line 132." (Align.pl is my slightly
>>> modified example of the Compara Tutoraial code.)
>>> As these are slightly modified perl scripts from the documantation, the
>>> line
>>> numbers may be variable.
>>> I can print out the genome_dbs, and it gives me a list of genome names
>>> (hash
>>> tables) though it appears that is problematic in the Align.pl script.
>>> in spite of the fact that just previously to that call I dumped
>>> "genome_dbs"
>>> and got back some 25 hash tables (expected).  I believe this occurs
>>> whether
>>> one is comparing "human:mouse" or the more complex species set I have
>>> outlined above.
>>> Has anyone else attempted to run the code documented in the Ensembl API
>>> Tutorial?
>>> Any suggestions as to what direction to go in would be appreciated -- when
>>> one is trying to copy code out of a tutorial and it fails its kind of hard
>>> to know where to go.)
>>> There do appear to be some problems in the specifications of a Compara
>>> version/database and there don't appear to be a lot of resources informing
>>> one of what resources are currently available.
>>> Robert
>>> 1. http://pre.ensembl.org/info/docs/api/compara/compara_tutorial.html
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> --
>> Andreas Kähäri, Ensembl Software Developer
>> European Bioinformatics Institute (EMBL-EBI)
>> Wellcome Trust Genome Campus, Hinxton
>> Cambridge CB10 1SD, United Kingdom
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