Bio::SearchIO::psl - A parser for PSL output (UCSC) use Bio::SearchIO; my $parser = new Bio::SearchIO(-file => 'file.psl', -format => 'psl'); while( my $result = $parser->next_result ) { } This is a SearchIO driver for PSL format. PSL format is documented here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL By default it assumes PSL output came from BLAT you can override that by specifying -program_name => 'BLASTZ' when initializing the SearchIO object.

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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 email or the web: http://bugzilla.bioperl.org/ Email jason-at-bioperl-dot-org Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::SearchIO::psl(); Function: Builds a new Bio::SearchIO::psl object Returns : an instance of Bio::SearchIO::psl Args :

next_result
Title : next_result Usage : my $result = $parser->next_result Function: Parse the next result from the data stream Returns : L<Bio::Search::Result::ResultI> Args : none

start_element
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'

end_element
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'

element
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'

characters
Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string

_mode
Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional)

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 'in' because within can be tested for a whole block. Returns : boolean Args : string element name

start_document
Title : start_document Usage : $eventgenerator->start_document Function: Handles 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 we have processed Returns : integer Args : none

program_name
Title : program_name Usage : $obj->program_name($newval) Function: Get/Set the program name Returns : value of program_name (a scalar) Args : on set, new value (a scalar or undef, optional)