[Bioperl-guts-l] [Bug 2197] Bio::Species throws if species name is synonym of lineage

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Jan 29 14:52:49 EST 2007


------- Comment #7 from roy at colibase.bham.ac.uk  2007-01-29 14:52 -------
> Thanks for catching that Roy!  It's been a hectic day....
> I haven't been able to replicate this using bioperl-live; Sendu made  
> a patch to Bio::Species which seems to work well.  Have you tried it?

I'm using the released BioPerl 1.52 which includes the patch- it's a different
problem. Playing around, it only manifests itself when storing in BioSQL using
bp_load_seqdatabase.pl, so I think the problems are in bioperl-db rather than
Bio::Species. Seems like there is a database lookup somewhere that overwrites
the species name but not the classification (or maybe vice versa).

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