[Bioperl-l] Indexing HMMER reports

Toni Hermoso Pulido toniher at softcatala.cat
Tue Mar 10 09:49:35 EDT 2009

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

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

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