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.

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 : integer
Args    : none

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq