[Bioperl-l] Bio::SearchIO::hmmer hsp behaviour

[Selvi Kadirvel]

Chris:

I just tried it out, and it looks like this solution works fine for  
me. Thank you for the fix!

-Selvi


On Jul 5, 2006, at 11:36 AM, Chris Fields wrote:

> Okay, I managed to figure out what the problem was.  I committed a  
> fix in
> CVS for the initial bug (Selvi's missing hits).  Still has one HSP  
> per hit
> for now; I think it will take a bit more effort to get a BLAST-like  
> multi
> HSP/hit up and running.
>
> Selvi, update from CVS to see if that works.
>
> Chris
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Chris Fields
>> Sent: Friday, June 30, 2006 12:44 PM
>> To: Sendu Bala; Jason Stajich
>> Cc: bioperl-l at lists.open-bio.org list
>> Subject: Re: [Bioperl-l] Bio::SearchIO::hmmer hsp behaviour
>>
>> I'll try looking at it this weekend.  A suggested workaround is to
>> either try setting -A for no alignments or setting it to a high
>> number to retrieve all of them.  It's pretty serious as the error
>> silently dumps those domains, so for those using automated annotation
>> pipelines would miss it unless they are also checking the raw output.
>>
>> You could design a SearchIO::hmmpfam parser then expand it to take in
>> hmmsearch output at a later point, or keep them separate.  I like the
>> idea of having modules that are more specific about what they parse;
>> seems at some point you reach serious code bloat and maintenance
>> becomes an issue.  Look at SearchIO::blast; it parses various text
>> BLAST output very well but with some serious obfuscation.  Just don't
>> know how productive it would be to separate out the PSI-BLAST and
>> bl2seq stuff since they are pretty close to a standard BLAST
>> report... oh well.
>>
>> To Jason : good luck on your move.  Drop  us a line here to let us
>> know everything went well.
>>
>> Chris
>>
>> On Jun 30, 2006, at 11:14 AM, Sendu Bala wrote:
>>
>>> Chris Fields wrote:
>>>> It may have been just simpler to have it be one HSP (domain) per  
>>>> Hit
>>>> (model) as that's how the reports are generated.  My reasoning was
>>>> that
>>>> using the one domain per model made sense based on what you are
>>>> actually
>>>> trying to do, which is annotate the sequence based on the order the
>>>> domain appears.  Most others may not view it that way, which is  
>>>> fine.
>>>> One can always gather the relevant HSP's, convert to seqfeatures,
>>>> then
>>>> sort them if order is important, I suppose.
>>>>
>>>> I would say, if the overall consensus is to modify it to have
>>>> multiple
>>>> domain hits per model (similar to BLAST) then Sendu should go
>>>> ahead and
>>>> make those changes then announce it on the list so no one can gripe
>>>> about it later.  My main concern was not changing things so
>>>> dramatically
>>>> that it'll break for someone
>>>
>>> Going on your earlier suggestion, I was thinking about making
>>> SearchIO::hmmpfam instead, which would get used if you set the
>>> format to
>>> 'hmmpfam' instead of the generic 'hmmer' when making a SearchIO. I
>>> suppose I would make a SearchIO::hmmsearch as well, if necessary.
>>>
>>>
>>> [...]
>>>> that the reported bug about missing hits (Bug 2036) is fixed as  
>>>> well.
>>>
>>> However, having never made a SearchIO plugin before, it will be some
>>> time before I get my head around it. I'll want to make one the  
>>> current
>>> HOWTO:SearchIO way before I can think about doing it a better way
>>> (hashes) as well. So I can say I'll make a move on this at some
>>> point in
>>> the future, but if someone wants to fix Bug 2036 in the mean time,
>>> they
>>> are welcome to. Again as suggested, my priority is Bio::Map right  
>>> now.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
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>
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