[Bioperl-l] parsing hmmpfam reports

[Marc Logghe]

Hi Stephan,
AFAIK one can obtain the model string using the name() method.
Example code:

         Build a Hmmpfam factory

         my @params = ('DB'=>$dbfile,'E'=>0.0001);
         my $factory = Bio::Tools::Run::Hmmpfam->new($params);

         # Pass the factory a Bio::Seq object or a file name

         # returns a Bio::SearchIO object
         my $search = $factory->run($seq);

         while (my $result = $searchio->next_result){
          while(my $hit = $result->next_hit){
              print $hit->$_, "\n" for qw(name description rank);
           }
          }
         }

HTH,
Marc

> -----Original Message-----
> From: stephan.rosecker at ish.de [mailto:stephan.rosecker at ish.de]
> Sent: vrijdag 30 april 2004 13:07
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] parsing hmmpfam reports
> 
> 
> Hi,
> 
> i'm looking for a method to get the family classification 
> (family model)
> in an hmmpfam report.Maybe some usefull stuff in
> Bio::Search::Result::GenericResult ?
> 
> For example:
> 
> hmmpfam - search one or more sequences against HMM database
> HMMER 2.3.2 (Oct 2003)
> Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
> Freely distributed under the GNU General Public License (GPL)
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
> - - - - -
> HMM file:                 nst.hmms
> Sequence file:            uniprot_sprot.dat
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> Query sequence: 128U_DROME
> Accession:      P32234
> Description:    GTP-binding protein 128UP.
> 
> Scores for sequence family classification (score includes all 
> domains):
> Model    Description                                    Score
> E-value  N
> -------- -----------                                    ----- 
>    -------
> ---
> Drg                                                     639.4
> 1.6e-191   1
> 
> Parsed for domains:
> Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
> -------- ------- ----- -----    ----- -----      -----  -------
> Drg        1/1       4   367 ..     1   375 []   639.4 1.6e-191
> 
> .
> .
> .
> 
> 
> What i want is the "Drg" string.
> 
> 
> Regards,
> stephan
> 
> 
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