Bio::SearchIO::hmmer3(3)

NAME
Bio::SearchIO::hmmer3

SYNOPSIS
use Bio::SearchIO;

my $searchio = Bio::SearchIO->new(
    -format => 'hmmer',
    -version => 3,
    -file => 'hmmsearch.out' );

my $result = $searchio->next_result; my $hit = $result->next_hit; print $hit->name, $hit->description, $hit->significance,
      $hit->score, "\n";

my $hsp = $hit->next_hsp; print $hsp->start('hit'), $hsp->end('hit'), $hsp->start('query'),
      $hsp->end('query'), "\n";

DESCRIPTION
Code to parse output from hmmsearch, hmmscan, and nhmmer, compatible with both version 2 and version 3 of the HMMER package from <http://hmmer.org>.

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Thomas Sharpton
Email thomas.sharpton@gmail.com

Describe contact details here

CONTRIBUTORS
Additional contributors names and emails here

briano at bioteam.net

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  next_result
 Title   : next_result
 Usage   : my $hit = $searchio->next_result;
 Function: Returns the next Result from a search
 Returns : Bio::Search::Result::ResultI object
 Args    : none

  start_element
 Title   : start_element
 Usage   : $eventgenerator->start_element
 Function: Handles a start event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'

  end_element
 Title   : end_element
 Usage   : $eventgeneartor->end_element
 Function: Handles and end element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'

  element
 Title   : element
 Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
 Function: Convenience method that calls start_element, characters, end_element
 Returns : none
 Args    : Hash ref with the keys 'Name' and 'Data'

  get_from_element
 Title   : get_from_element
 Usage   : $self->get_from_element('HSP-hit_start');
 Function: Convenience method to retrieve data from '_values' hash
 Returns : string
 Args    : key

  characters
 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string

  within_element
 Title   : within_element
 Usage   : if( $eventgenerator->within_element( $element ) ) {}
 Function: Test if we are within a particular element
           This is different than 'in' because within can be tested for
           a whole block
 Returns : boolean
 Args    : string element name

  in_element
 Title   : in_element
 Usage   : if( $eventgenerator->in_element( $element ) ) {}
 Function: Test if we are in a particular element
           This is different than 'within' because 'in' only
           tests its immediate parent
 Returns : boolean
 Args    : string element name

  start_document
 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handle a start document event
 Returns : none
 Args    : none

  end_document
 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none

  result_count
 Title   : result_count
 Usage   : my $count = $searchio->result_count
 Function: Returns the number of results processed
 Returns : interger
 Args    : none