[Bioperl-l] HMMER 3 update

[Brian Osborne]

Jason,

Done, and I added a strand() method to Bio::Search::HSP::GenericHSP. There's a lot of inheritance in these "HSP" modules but it looks like this is the right place, as judged by the other methods in the module.

Double-checked all the _other_ SearchIO tests, they're all passing.

BIO



On Jul 15, 2013, at 12:30 AM, Jason Stajich <jason.stajich at gmail.com> wrote:

> Brian -
> 
> I think a branch is good idea, probably just from master as I presume this code will be too new to weave into the v1 branch. 
> 
> However, I'm still not clear on how the new packaging is going to go - but I presume there will be a SearchIO package that we'd update and release when needed? Is there any move to split that off - I know we had settled on the idea that the essential bits of a core would be at least some sequence and blast/homology search parsers.
> 
> But would more 'exotic' parsers live in their own package or all things SearchIO would go together?
> 
> Glad to see this being work on Brian -- will also have to make sure to capture strand info which we didn't have to deal with for protein queries.
> 
> Jason
> On Jul 12, 2013, at 1:05 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> 
>> bioperl,
>> 
>> HMMER 3.1 contains a new program called nhmmer, its output is a bit different from the existing so I need to edit SearchIO::hmmer3.
>> 
>> Create a new branch for this?
>> 
>> Brian O.
>> 
>> 
>> 
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> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 
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