[Bioperl-l] Ensembl problems

Chris Fields cjfields at illinois.edu
Sat Jan 9 17:01:19 EST 2010


Ensembl errors probably should be redirected to the ensembl mail list.  I can't speak to the problems with it (they appear specific to the Ensembl tool set).


On Jan 9, 2010, at 2:27 PM, Robert Bradbury wrote:

> I am trying to get the examples provided by EMBL/Ensembl to work and am
> encountering problems.
> 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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