Bio::Map::GeneRelative(3pm)				User Contributed Perl Documentation			       Bio::Map::GeneRelative(3pm)

NAME

       Bio::Map::GeneRelative - Represents being relative to named sub-regions of a
				gene.

SYNOPSIS

	   use Bio::Map::GeneRelative;

	   # say that a somthing will have a position relative to the start of the
	   # gene on map
	   my $rel = Bio::Map::GeneRelative->new(-gene => 0);

	   # or that something will be relative to the third transcript of a gene
	   # on a map
	   $rel = Bio::Map::GeneRelative->new(-transcript => 3);

	   # or to the 5th intron of the default transcript
	   $rel = Bio::Map::GeneRelative->new(-intron => [0, 5]);

	   # use the $rel as normal; see L<Bio::Map::Relative>

DESCRIPTION

       Be able to say that a given position is relative to some standard part of a gene.

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/

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

APPENDIX

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

   new
	Title	: new
	Usage	: my $relative = Bio::Map::Relative->new();
	Function: Build a new Bio::Map::Relative object.
	Returns : Bio::Map::Relative object
	Args	: -gene => int	     : coordinates are relative to the int'th base
				       downstream of the Position's map's gene
				       [default is gene => 0, ie. relative to the
				       start of the gene],
		  -transcript => int : or relative to the start of the int'th
				       transcript of the Position's map's gene,
		  -exon => [i, n]    : or relative to the start of the n'th
				       transcript's i'th exon,
		  -intron => [i, n]  : or intron,
		  -coding => int     : or the start of the int'th transcript's coding
				       region.

		  -description => string : Free text description of what this relative
					   describes

		  (To say a Position is relative to something and upstream of it,
		   the Position's start() co-ordinate should be set negative)
		  In all cases, a transcript number of 0 means the active transcript.

   absolute_conversion
	Title	: absolute_conversion
	Usage	: my $absolute_coord = $relative->absolute_conversion($pos);
	Function: Convert the start co-ordinate of the supplied position into a number
		  relative to the start of its map.
	Returns : scalar number
	Args	: Bio::Map::PositionI object

   type
	Title	: type
	Usage	: my $type = $relative->type();
	Function: Get the type of thing we are relative to. The types correspond
		  to a method name, so the value of what we are relative to can
		  subsequently be found by $value = $relative->$type;

		  Note that type is set by the last method that was set, or during
		  new().

	Returns : 'gene', 'transcript', 'exon', 'intron' or 'coding'
	Args	: none

   gene
	Title	: gene
	Usage	: my $int = $relative->gene();
		  $relative->gene($int);
	Function: Get/set the distance from the start of the gene that the Position's
		  co-ordiantes are relative to.
	Returns : int
	Args	: none to get, OR
		  int to set; a value of 0 means relative to the start of the gene.

   transcript
	Title	: transcript
	Usage	: my $int = $relative->transcript();
		  $relative->transcript($int);
	Function: Get/set which transcript of the Position's map's gene the Position's
		  co-ordinates are relative to.
	Returns : int
	Args	: none to get, OR
		  int to set; a value of 0 means the active (default) transcript.

   exon
	Title	: exon
	Usage	: my ($exon_number, $transcript_number) = @{$relative->exon()};
		  $relative->exon($exon_number, $transcript_number);
	Function: Get/set which exon of which transcript of the Position's map's gene
		  the Position's co-ordinates are relative to.
	Returns : reference to list with two ints, exon number and transcript number
	Args	: none to get, OR
		  int (exon number) AND int (transcript number) to set. The second int
		  is optional and defaults to 0 (meaning default/active transcript).

   intron
	Title	: intron
	Usage	: my ($intron_number, $transcript_number) = @{$relative->intron()};
		  $relative->intron($intron_number, $transcript_number);
	Function: Get/set which intron of which transcript of the Position's map's gene
		  the Position's co-ordinates are relative to.
	Returns : reference to list with two ints, intron number and transcript number
	Args	: none to get, OR
		  int (intron number) AND int (transcript number) to set. The second
		  int is optional and defaults to 0 (meaning default/active
		  transcript).

   coding
	Title	: coding
	Usage	: my $transcript_number = $relative->coding;
		  $relative->coding($transcript_number);
	Function: Get/set which transcript's coding region of the Position's map's gene
		  the Position's co-ordinates are relative to.
	Returns : int
	Args	: none to get, OR
		  int to set (the transcript number, see transcript())

perl v5.14.2							    2012-03-02					       Bio::Map::GeneRelative(3pm)