[Bioperl-l] Indexing HMMER reports

Mauricio Herrera Cuadra mauricio at open-bio.org
Tue Mar 10 01:39:23 EDT 2009


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,
> 


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