Brian Osborne | 16 Jul 18:36 2013
Picon
Picon

Re: HMMER 3 update

Done.

On Jul 16, 2013, at 12:30 PM, "Fields, Christopher J" <cjfields <at> illinois.edu> wrote:

> 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
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l <at> lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l <at> lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

Gmane