Bio::SearchIO::psl(3)

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:

  http://bugzilla.open-bio.org/

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)