[Bioperl-l] Ensembl problems

Andreas Kähäri ak at ebi.ac.uk
Sat Jan 9 17:01:21 EST 2010


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
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> 

-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom


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