Bio::SearchIO::Writer::GbrowseGFF - Interface for outputting parsed search results in Gbrowse GFF format use Bio::SearchIO; my $in = new Bio::SearchIO(-file => 'result.blast', -format => 'blast'); my $out = new Bio::SearchIO(-output_format => 'GbrowseGFF', -file => ">result.gff"); while( my $r = $in->next_result ) { $out->write_result($r); } This writer produces Gbrowse flavour GFF from a Search::Result object. Email markw-at-illuminae-dot-com

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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.bioperl.org/ 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::Writer::GbrowseGFF(@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 10)

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 : @args = none at present... 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