Bio::SearchIO::psl(3) User Contributed Perl DocumentationBio::SearchIO::psl(3)NAMEBio::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)
perl v5.14.1 2011-07-22 Bio::SearchIO::psl(3)
