| Bio::SearchIO::wise(3pm) | User Contributed Perl Documentation | Bio::SearchIO::wise(3pm) |
Bio::SearchIO::wise - Parsing of wise output as alignments
use Bio::SearchIO;
my $parser = Bio::SearchIO->new(-file => 'file.genewise',
-format => 'wise',
-wisetype=> 'genewise');
while( my $result = $parser->next_result ) {}
This object parsers Wise output using Bio::Tools::Genewise or Bio::Tools::Genomewise as a helper.
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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 = Bio::SearchIO::wise->new(); Function: Builds a new Bio::SearchIO::wise object Returns : an instance of Bio::SearchIO::wise Args : -wise => a Bio::Tools::Genewise or Bio::Tools::Genomewise object
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 'in' because within can be tested
for a whole block.
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 : wise Usage : $obj->wise($newval) Function: Get/Set the Wise object parser Returns : value of wise (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : wisetype Usage : $obj->wisetype($newval) Function: Wise program type Returns : value of wisetype (a scalar) Args : on set, new value (a scalar or undef, optional)
| 2018-10-27 | perl v5.26.2 |