[Bioperl-l] Indexing HMMER reports

Brian Osborne bosborne11 at verizon.net
Tue Mar 10 10:02:48 EDT 2009


Toni,

It's not designed to parse the contents, that's the job of SearchIO.  
Check the SearchIO HOWTO, it may be informative.

You would use this if, for example, you had many hmmsearch results and  
you had the corresponding ids and you wanted to retrieve the results  
quickly and directly.

Brian O.

On Mar 10, 2009, at 9:49 AM, Toni Hermoso Pulido wrote:

> Thanks Mauricio. I will take a look at your script and I will adapt my
> own ones.
>
> As Jason commented before, as this module is documented, it only  
> indexes
> reports (not their contents) and so it's not very useful in the
> end.
>
> En/na Mauricio Herrera Cuadra ha escrit:
>> I've been kind of disconnected from this stuff for a while but I  
>> "think"
>> you could use (or take ideas from) a script of mine in the core
>> distribution:
>>
>> http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/scripts/searchio/parse_hmmsearch.PLS
>>
>>
>> If you give the script a file with the list of reports to parse, it  
>> will
>> print out most of the useful data from them. `bp_parse_hmmsearch.pl  
>> -h`
>> will provide more help about its use.
>>
>> Mauricio.
>>
>>
>> Toni Hermoso Pulido wrote:
>>> Hello,
>>>
>>> I'm trying to index HMMER reports using:
>>> http://www.bioperl.org/wiki/Module:Bio::Index::Hmmer
>>>
>>> However, I have not found enough information in the module code
>>> examples for being able to index and get info from those reports.
>>>
>>> I would like to get HSP alignments associated to hit accession codes
>>> from reports distributed in several files.
>>>
>>> Does anyone have experience on this?
>>>
>>> After dumping variables, I think I'm just indexing report files, but
>>> not its contents.
>>>
>>> Best regards,
>>>
>
>
> -- 
> Toni Hermoso Pulido
> http://www.cau.cat
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> Bioperl-l at lists.open-bio.org
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