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.
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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
To install Bio::SearchIO::hmmer, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::SearchIO::hmmer
CPAN shell
perl -MCPAN -e shell install Bio::SearchIO::hmmer
For more information on module installation, please visit the detailed CPAN module installation guide.