Fields, Christopher J | 16 Jul 18:30 2013

Re: HMMER 3 update

Works for me as well.  Brian, go ahead and merge into master; I can merge into v1_cherry (which will
eventually make it's way into v1 and a new release, still working through a few bugs).

chris

On Jul 16, 2013, at 10:18 AM, Brian Osborne <bosborne11 <at> verizon.net> wrote:

> 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.
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l <at> lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> Jason Stajich
>> jason.stajich <at> gmail.com
>> jason <at> bioperl.org
>> 
>> 
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> 
> 
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Gmane