Provided by: libbio-perl-perl_1.7.2-2_all bug


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


         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 ) {


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

AUTHOR Mark Wilkinson

       Email markw-at-illuminae-dot-com


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


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       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        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.)

        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
                                  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

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

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

        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    : makes no changes to the default filter code