| Bio::SearchIO::hmmer3(3pm) | User Contributed Perl Documentation | Bio::SearchIO::hmmer3(3pm) |
Bio::SearchIO::hmmer3
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";
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>.
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
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.
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
Email thomas.sharpton@gmail.com
Describe contact details here
Additional contributors names and emails here
briano at bioteam.net
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : start_element Usage : $eventgenerator->start_element Function: Handles a start event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name'
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'
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'
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
Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string
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
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
Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none
Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none
Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results processed Returns : integer Args : none
| 2018-10-27 | perl v5.26.2 |