[maker-devel] BioPerl Bio::Tools::CodonTable changes

[Carson Holt]

Actually since I wanted to keep compatibility with old versions of BioPerl, I’ve been using the add_table method to just insert the tabled I need.  Then I select it using the id method.

But I think I like the idea of making the strictly canonical codon table be table 0, since having a strictly canonical codon table in BioPerl seems rather important.

Thanks,
Carson




> On Nov 13, 2014, at 9:34 PM, Fields, Christopher J <cjfields at illinois.edu> wrote:
> 
> Carson,
> 
> Just a note that we need to address a specific hack added last year in BioPerl for MAKER re: ‘strict’ codon tables.  I added a new one to the end of the list, not thinking that more would eventually be added, and that time has now come:
> 
> https://github.com/bioperl/bioperl-live/issues/90
> 
> I’m not sure how MAKER is setting the table, but if it’s by using the codon table # that will likely subtly break as it will now point to the new codon table from NCBI.
> 
> chris
>