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Gmane
From: Brian Osborne <bosborne11 <at> verizon.net>
Subject: Re: HMMER 3 update
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 18th July 2013 13:10:39 UTC (over 3 years ago)
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  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,  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
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> [email protected]
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> _______________________________________________
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> 
> _______________________________________________
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