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Gmane
From: Florent Angly <florent.angly <at> gmail.com>
Subject: Re: HMMER 3 update
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 18th July 2013 07:32:51 UTC (over 3 years ago)
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,  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,  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,  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"
 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 
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 <[email protected]>
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 
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
>>>>> [email protected]
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> Jason Stajich
>>>> [email protected]
>>>> [email protected]
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> [email protected]
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> _______________________________________________
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>
> _______________________________________________
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