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Manual Reference Pages  -  BIO::SEARCHIO::PSL (3)

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NAME

Bio::SearchIO::psl - A parser for PSL output (UCSC)

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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)



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