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Bio::FeatureIO::bed(3)User Contributed Perl DocumentatioBio::FeatureIO::bed(3)

NAME
       Bio::FeatureIO::bed - read/write	features from UCSC BED format

SYNOPSIS
	 my $in	= Bio::FeatureIO(-format => 'bed', -file => 'file.bed');
	 for my	$feat ($in->next_feature) {
	   # do	something with $feat (a	Bio::SeqFeature::Annotated object)
	 }

	 my $out = Bio::FeatureIO(-format=>'bed');
	 for my	$feat ($seq->get_seqFeatures) {
	   $out->write_feature($feat);
	 }

DESCRIPTION
       See <http://www.genome.ucsc.edu/goldenPath/help/customTrack.html#BED>.

       Currently for read and write only the first 6 fields (chr, start, end,
       name, score, strand) are	supported.

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:

	 http://bugzilla.open-bio.org/

AUTHOR - Allen Day
       Email allenday@ucla.edu

CONTRIBUTORS
       Sendu Bala, bix@sendu.me.uk

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   _initialize
	Title	: _initialize
	Function: initializes BED for reading/writing
	Args	: all optional:
		  name		description
		  ----------------------------------------------------------
		  -name		the name for the BED track, stored in header
				name defaults to localtime()
		  -description	the description	for the	BED track, stored in
				header.	 defaults to localtime().
		  -use_score	whether	or not the score attribute of
				features should	be used	when rendering them.
				the higher the score the darker	the color.
				defaults to 0 (false)

   use_score
	Title	: use_score
	Usage	: $obj->use_score($newval)
	Function: should score be used to adjust feature color when rendering?	set to true if so.
	Example	:
	Returns	: value	of use_score (a	scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   name
	Title	: name
	Usage	: $obj->name($newval)
	Function: name of BED track
	Example	:
	Returns	: value	of name	(a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   description
	Title	: description
	Usage	: $obj->description($newval)
	Function: description of BED track
	Example	:
	Returns	: value	of description (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

perl v5.32.0			  2014-09-05		Bio::FeatureIO::bed(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Allen Day | CONTRIBUTORS | APPENDIX

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