Christopher Fields > BioPerl > Bio::SearchIO::Writer::GbrowseGFF



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Module Version: 1.006924   Source  


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
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