NAME

       Bio::SearchIO::Writer::GbrowseGFF - Interface for outputting parsed search results in
       Gbrowse GFF format

SYNOPSIS

         use Bio::SearchIO;
         my $in = Bio::SearchIO->new(-file   => 'result.blast',
                                    -format => 'blast');
         my $out = Bio::SearchIO->new(-output_format  => 'GbrowseGFF',
                                     -output_cigar   => 1,
                                     -output_signif  => 1,
                                     -file           => ">result.gff");
         while( my $r = $in->next_result ) {
           $out->write_result($r);
         }

DESCRIPTION

       This writer produces Gbrowse flavour GFF from a Search::Result object.

AUTHOR Mark Wilkinson

       Email markw-at-illuminae-dot-com

CONTRIBUTORS

       Susan Miller sjmiller at email-DOT-arizon-DOT-edu Jason Stajich jason at bioperl-dot-org

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/

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::Writer::GbrowseGFF->new(@args);
        Function: Builds a new Bio::SearchIO::Writer::GbrowseGFF object
        Returns : an instance of Bio::SearchIO::Writer::GbrowseGFF
        Args    :  -e_value => 10   : set e_value parsing cutoff (default undef)
                   (note the -e_value flag is deprecated.)

   to_string
        Purpose   : Produce the Gbrowse format GFF lines for a Result
        Usage     : print $writer->to_string( $result_obj, @args);
        Argument  : $result_obj = A Bio::Search::Result::ResultI object
                    -version => 1|2|2.5|3  ; the GFF format you want to output (default 3)
                    -match_tag => match|cDNA_match|EST_match|translated_nucleotide_match
                                  nucleotide_to_protein_match|nucleotide_motif
                                  This is the SO term to be placed in GFF column 3.
                    -prefix => String to prefix the group by, default is EST
                               (see %Defaults class variable) A default can also
                               be set on object init
        Returns   : String containing data for each search Result or any of its
                  : sub-objects (Hits and HSPs).
        Throws    : n/a

   start_report
        Title   : start_report
        Usage   : $self->start_report()
        Function: has no function, returns nothing
        Returns : empty string
        Args    : none

   end_report
        Title   : end_report
        Usage   : $self->end_report()
        Function: has no function, returns nothing
        Returns : empty string
        Args    : none

   filter
        Title   : filter
        Usage   : $writer->filter('hsp', \&hsp_filter);
        Function: Filter out either at HSP,Hit,or Result level
        Returns : none
        Args    : string => data type,
                  CODE reference
        Note    : GbrowseGFF.pm makes no changes to the default filter code