[Bioperl-l] parsing hmmpfam reports

[Jason Stajich]

YOu want $hit->name see the SearchIO HOWTO.

On Fri, 30 Apr 2004 stephan.rosecker at ish.de wrote:

> 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
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu