[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?  


More information about the Bioperl-l mailing list