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

[Fields, Christopher J]

Okay, just wanted to make sure that a change in this wouldn’t break MAKER.  

chris

On Nov 14, 2014, at 10:46 AM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>> 
>