[Bioperl-l] Indexing HMMER reports

Chris Fields cjfields at illinois.edu
Tue Mar 10 00:01:39 EDT 2009


I'm not familiar with that one, but I assume the indexing is very  
likely by the query ID (similar to BLAST report indexing, which I've  
worked on).  So, you would index the report first:

--------------------------------
#!/usr/bin/perl -w
use strict;
use Bio::Index::Hmmer;
my $indexfile = shift;
my $index = Bio::Index::Hmmer->new(
     -filename => $indexfile,
     -write_flag => 1
);
$index->make_index(@ARGV);
--------------------------------

Then, retrieve the HMMER report using the query ID and fetch_report(),  
which just advances the file pointer to the start of the indicated  
report prior to parsing, and returns the Bio::Search::Result::ResultI,  
I believe.

chris

On Mar 9, 2009, at 7:58 PM, 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



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