NAME

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

SYNOPSIS

  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);
  }

DESCRIPTION

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

AUTHOR Mark Wilkinson

Email markw-at-illuminae-dot-com

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/MailList.shtml  - About the mailing lists

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/

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 = 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