Bio::SearchIO::hmmer - A parser for HMMER output (hmmpfam, hmmsearch)
# do not use this class directly it is available through Bio::SearchIO use Bio::SearchIO; my $in = new Bio::SearchIO(-format => 'hmmer', -file => 't/data/L77119.hmmer'); while( my $result = $in->next_result ) { # this is a Bio::Search::Result::HMMERResult object print $result->query_name(), " for HMM ", $result->hmm_name(), "\n"; while( my $hit = $result->next_hit ) { print $hit->name(), "\n"; while( my $hsp = $hit->next_hsp ) { print "length is ", $hsp->length(), "\n"; } } }
This object implements a parser for HMMER output.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::SearchIO::hmmer(); Function: Builds a new Bio::SearchIO::hmmer object Returns : Bio::SearchIO::hmmer Args : -fh/-file => HMMER filename -format => 'hmmer'
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 element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name'
Title : start_element Usage : $eventgenerator->end_element Function: Handles an 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: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data'
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 immediete 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 we have processed Returns : integer Args : none
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.