[Bioperl-l] Ensembl problems

Robert Bradbury robert.bradbury at gmail.com
Sun Jan 10 14:47:00 EST 2010

As it turns out the example from the file I cited (the compara API
tutorial does work).  The code that I started with may have been from
a "MS-WORD" document distributed with the documentation (which could
quite well be out-of-date).

But even the corrected code does not work for various uncommon
comparisons between species (which they may not have archived in
Ensembl).  I also don't understand enough about the functions yet as
to whether they are comparing the same regions from the same
chromosomes that just happen to be identical or whether they are
comparing the same region with a homologous region on a different
chromosome (i.e. conserved genes).  I'm going to have to dig into this
some more to figure out what is going on.

Thanks for the pointers, I'll refer future questions to the Ensembl

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


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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