Florent Angly | 18 Jul 09:32 2013
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Re: HMMER 3 update

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