[Bioperl-l] HMMER 3 update

[Florent Angly]

Okidoki. Well done and thank you,
Florent

On 18/07/13 23:10, Brian Osborne wrote:
> Florent,
>
> Yes, I see it. This block of code is described as "not currently fully implemented", I think it was always giving this warning. Fixed now.
>
> This parser is getting a bit disorganized as new apps get added, maybe I'll reorganize it at some point, but not now.
>
> Thanks for that,
>
> Brian O.
>
>
> On Jul 18, 2013, at 3:32 AM, Florent Angly <florent.angly at gmail.com> wrote:
>
>> Hi Brian,
>>
>> One line of the hmmer3 module gives me a warning:
>>> $ perl -w -I lib ./t/SearchIO/hmmer.t
>>> [...]
>>> ok 117 - Check if correct searchio object is returned
>>> Use of uninitialized value $hitid in hash element at Bio/SearchIO/hmmer3.pm line 416, <GEN17> line 16.
>>> [...]
>>> ok 285 - Check if loading hmmscan output via the hmm3 parser directly works
>>> Use of uninitialized value $hitid in hash element at Bio/SearchIO/hmmer3.pm line 416, <GEN35> line 16.
>>> [...]
>>> ok 293 - Check if selecting the correct hmmscan parser using -version works
>>> Use of uninitialized value $hitid in hash element at Bio/SearchIO/hmmer3.pm line 416, <GEN47> line 16.
>> This happens because it tries to split() to get record information from a line that looks like:
>>>   ------ inclusion threshold ------
>> It's probably easy to fix for someone familiar with the code logic.
>> Best,
>>
>> Florent
>>
>>
>>
>>
>> On 17/07/13 02:36, Brian Osborne wrote:
>>> 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
>>> _______________________________________________
>>> 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