[Bioperl-l] bioperl-db Species question
cjfields at uiuc.edu
Wed Jan 31 16:23:52 UTC 2007
I have a couple of quick bioperl-db questions; no hurry if you have
your hands full.
I was working on fixing a bioperl-db bug for Roy, which is also
related to Brian's bug:
Two things popped up:
1) As Sendu alluded to in Brian's bug report (bug 2092),
Bio::DB::BioSQL::SpeciesAdaptor has the current behavior of storing
Bio::Species data by genus/species names (single name for each) via
resetting classification(), which is inconsistent with Sendu's
Bio::Species/Bio::Taxon changes. Currently, Bio::Species stores
names strictly by genus/species node names, where the species node
name normally also contains the genus name.
I know where to make initial changes if we want to use node names in
bioperl-db (SpeciesAdaptor::populate_from_row), but this currently
break some bioperl-db species tests (02species.t). I can also see
this being a big headache, though I couldn't find anything that
indicates doing so isn't BioSQL-compliant. What would be the best
way to go here?
2) Somewhat related: should we be running strict node name checks
using throw() in Bio::Species at all times? There is no current
workaround using FORCE, as is suggested in Bio::Species POD. This
currently seems to cause more problems than it's worth and sometimes
throws even when running tax lookups with bioperl-db (Roy's bug). I
have changed the throw() to a warn() for the time being.
In the meantime, I am also converting all tests in bioperl-db to
Test::More (I'm about 3/4 through now); I'll add a copy of
Test::Simple to bioperl-db t/lib per Michael Schwern's instructions
JIC it isn't installed. Let me know if this is a problem.
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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