[Bioperl-l] module for description of sequence variants (where to place code)

[Fields, Christopher J]

On Mar 3, 2013, at 7:58 PM, Carnë Draug <carandraug+dev at gmail.com> wrote:

> On 25 February 2013 10:32, Andreas Leimbach
> <andreas.leimbach at uni-wuerzburg.de> wrote:
>> On 25.2.13 11:08, Carnė Draug wrote:
>>> 
>>> I'm writing a perl module to write a description of the variance
>>> between 2 sequences as described on
>>> http://www.hgvs.org/mutnomen/recs-prot.html
>>> 
>>> Basically, given 2 sequences, would returns something like "p.Lys2del
>>> p.His25_Met26insGln" if those are the differences. It also accounts
>>> for the existence of - characters on the sequences that may come from
>>> their alignment.
>>> 
>>> My question is, where on the project tree should I place the module?
>>> 
>>> Also, is there something already written that would convert from 1 to
>>> 3 letter code?
>>> 
>> for your last question:
>> You can convert aa strings from one to three letter code with
>> 'Bio::SeqUtils'.
> 
> Thank you. I have never used Bio::SeqUtils. Not only does solve my
> problem, but also seems to be the right place to insert my code.
> 
> If no one objects, I'll add a new method to Bio::SeqUtils named
> "describe_mutation".
> 
> Carnë

I'm fine with that; at some point it might be worth thinking about whether we need to organize the various *Utils modules a bit better.  As most of these export methods, they would be good targets for reorganization at some point (maybe into a general Bio::Utils namespace).

chris