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Bio::SearchIO::Writer:UseroContributed PerBio::SearchIO::Writer::GbrowseGFF(3)

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-Bio::SearchIO::Writer::GbrowseGFF(3)

NAME | SYNOPSIS | DESCRIPTION | AUTHOR Mark Wilkinson | CONTRIBUTORS | FEEDBACK | APPENDIX

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