debian man page for bio::searchio::writer::gbrowsegff

Bio::SearchIO::Writer::GbrowseGFF(3pm)			User Contributed Perl Documentation		    Bio::SearchIO::Writer::GbrowseGFF(3pm)

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

perl v5.14.2							    2012-03-02				    Bio::SearchIO::Writer::GbrowseGFF(3pm)