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bio::searchio::psl(3pm) [debian man page]

Bio::SearchIO::psl(3pm) 				User Contributed Perl Documentation				   Bio::SearchIO::psl(3pm)

NAME
Bio::SearchIO::psl - A parser for PSL output (UCSC) SYNOPSIS
use Bio::SearchIO; my $parser = Bio::SearchIO->new(-file => 'file.psl', -format => 'psl'); while( my $result = $parser->next_result ) { } DESCRIPTION
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. FEEDBACK
Mailing Lists 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 Support 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. 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 the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::SearchIO::psl->new(); 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> or undef if no more results 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 : end_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : return value from the associated end_$type event handler 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) perl v5.14.2 2012-03-02 Bio::SearchIO::psl(3pm)
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