Reference

Bio::SearchIO::hmmer3(3pm)

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, phmmer 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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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 [email protected]

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 : integer
 Args    : none

History