/ 
bioperl-1.5.2_004-RCd
/ Bio::SearchIO::axt

NAME

Bio::SearchIO::axt - a parser for axt format reports

SYNOPSIS

use Bio::SearchIO;
my $parser = new Bio::SearchIO(-format => 'axt',
                               -file   => 't/data/report.blastz');
while( my $result = $parser->next_result ) {
  while( my $hit = $result->next_hit ) {
    while( my $hsp = $hit->next_hsp ) {
    }
  }
}

DESCRIPTION

This is a parser and event-generator for AXT format reports. BLASTZ reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally in LAV format but are commonly post-processed to AXT format; many precomputed BLASTZ reports, such as those found in the UCSC Genome Browser, are in AXT format. This parser will also parse any AXT format produced from any lav report and directly out of BLAT.

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

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.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 = new Bio::SearchIO::axt();
Function: Builds a new Bio::SearchIO::axt object 
Returns : an instance of Bio::SearchIO::axt
Args    :

next_result

Title   : next_result
Usage   : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
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