Brian Osborne | 18 Jul 15:10 2013
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Re: HMMER 3 update

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
>>>>> 
>>>>> 
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>>>> 
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Gmane