[Bioperl-l] Indexing HMMER reports

Chris Fields cjfields at illinois.edu
Tue Mar 10 10:22:42 EDT 2009


I wouldn't say it's not useful; just depends on your purpose.  The  
similar Bio::Index::Blast was very useful when I ran MCL clustering  
and needed to pull out a single BLAST report (out of a very large  
concatenated BLAST file) via the query ID.

Saying that, it would be nice to come up with a way to index the hit  
ID but that may require reconfiguring how parsed IDs are stored.

chris

On Mar 10, 2009, at 8:49 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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