Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse megablast reports
       (format 0)

SYNOPSIS

       # do not use this module directly

         use Bio::SearchIO;
         # for default format output from megablast
         my $in = Bio::SearchIO->new(-file   => 'file.mbl',
                                    -format => 'megablast',
                                    -report_format => 0);

         while( my $r = $in->next_result ) {
           while( my $hit = $r->next_hit ) {
             while( my $hsp = $hit->next_hsp ) {
             }
           }
         }

DESCRIPTION

       Beware!

       Because of the way megablast report format 0 is coded, realize that score means # gap
       characters + # mismatches for a HSP.

       The docs from NCBI regarding FORMAT 0 #   0: Produce one-line output for each alignment,
       in the form # #   'subject-id'=='[+-]query-id' (s_off q_off s_end q_end) score # #   Here
       subject(query)-id is a gi number, an accession or some other type of #   identifier found
       in the FASTA definition line of the respective sequence.  # #   + or - corresponds to same
       or different strand alignment.  # #   Score for non-affine gapping parameters means the
       total number of #   differences (mismatches + gap characters). For affine case it is the #
       actual (raw) score of the alignment.

       FORMAT 1 parsing has not been implemented FORMAT 2 parsing should work with the SearchIO
       'blast' parser

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.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::blast->new();
        Function: Builds a new Bio::SearchIO::blast object
        Returns : Bio::SearchIO::blast
        Args    : -fh/-file => filehandle/filename to BLAST file
                  -format   => 'blast'

   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

   report_format
        Title   : report_format
        Usage   : $obj->report_format($newval)
        Function: Get/Set the report_format value
        Returns : value of report_format (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   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