[Bioperl-l] Ensembl problems

Robert Bradbury robert.bradbury at gmail.com
Sat Jan 9 15:27:54 EST 2010

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

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
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.


1. http://pre.ensembl.org/info/docs/api/compara/compara_tutorial.html

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