[Bioperl-l] Memory requirements for conversion from embl to genbank

Chris Fields cjfields at uiuc.edu
Thu Aug 31 13:46:18 EDT 2006


...
> Bio::DB::Taxonomy::list should have been throwing an error before; it
> does now. It would be nicer really if embl.pm stopped adding to the
> classification array when it finds the end of one species
> classification, but then it's just guessing about how broken one
> particular file is.

I think the next area to check out post-1.5.2 (maybe pre-1.6) is
GenBank/EMBL/swiss parsing (all of them work pretty much the same way).
There is a lot of legacy code in there.
 
> I think the throw is good enough, let the user correct the file.

Agreed!  It's not Bioperl's job to fix bad sequences.  Did you want to close
the bug out?  

Chris




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