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

NAME

       Bio::Map::GenePosition - A typed position, suitable for modelling the various
				regions of a gene.

SYNOPSIS

	   use Bio::Map::GenePosition;
	   use Bio::Map::GeneMap;

	   # say that the first transcript of a particular gene on a particular map
	   # (species) is 1000bp long
	   my $map = Bio::Map:GeneMap->get(-universal_name => 'BRCA2',
					   -species => 'human');
	   my $gene = $map->gene;
	   Bio::Map::GenePosition->new(-map => $map,
				       -element => $gene,
				       -start => 0,
				       -length => 1000,
				       -type => 'transcript');

	   # say that the coding region of the gene starts 30bp into the first
	   # transcript
	   Bio::Map::GenePosition->new(-map => $map,
				       -element => $gene,
				       -start => 30,
				       -length => 600,
				       -type => 'coding');

	   # A GenePosition isa PositionWithSequence, so can have sequence associated
	   # with it
	   my $exon = Bio::Map::GenePosition->new(-map => $map,
				       -element => $gene,
				       -start => 0,
				       -type => 'exon',
				       -seq => 'ATGGGGTGGG');
	   my $length = $exon->length; # $length is 10

DESCRIPTION

       Define where various sub-regions (transcripts, exons, introns etc.) of a gene are. Do this so that you can then go onto to model other
       mappable elements as having positions 20bp upstream of transcript 2, or 10bp into intron 3 etc., all without having to know the absolute
       position of anything.

       See Bio::Map::GeneRelative and t/Map/Map.t for more example usage.

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 $obj = Bio::Map::GenePosition->new();
	Function: Builds a new Bio::Map::GenePosition object
	Returns : Bio::Map::GenePosition
	Args	: -map	    => Bio::Map::GeneMap object
		  -element  => Bio::Map::Gene object
		  -relative => Bio::Map::GeneRelative object
		  -type     => 'transcript|coding|exon|intron', REQUIRED
		  -seq	    => string, length of this string will set the length
			       of this position's range

		  * If this position has no range, or if a single value can describe
		    the range *
		  -value => scalar	       : something that describes the single
						 point position or range of this
						 Position, most likely an int

		  * Or if this position has a range, at least two of *
		  -start => int 	       : value of the start co-ordinate
		  -end => int		       : value of the end co-ordinate
		  -length => int	       : length of the range

   map
	Title	: map
	Usage	: my $map = $position->map();
		  $position->map($map);
	Function: Get/set the map the position is in.
	Returns : L<Bio::Map::MapI>
	Args	: none to get
		  new L<Bio::Map::MapI> to set

   element
	Title	: element
	Usage	: my $element = $position->element();
		  $position->element($element);
	Function: Get/set the element the position is for.
	Returns : L<Bio::Map::MappableI>
	Args	: none to get
		  new L<Bio::Map::MappableI> to set

   type
	Title	: type
	Usage	: my $type = $position->type();
		  $position->type($type);
	Function: Get/set the type of this position.
	Returns : string
	Args	: none to get, OR
		  string transcript|coding|exon|intron to set

   relative
	 Title	 : relative
	 Usage	 : my $relative = $position->relative();
		   $position->relative($relative);
	 Function: Get/set the thing this Position's coordinates (numerical(), start(),
		   end()) are relative to, as described by a RelativeI object.
	 Returns : Bio::Map::GeneRelative. The default GeneRelative returned has a
		   meaning that depends on the type() of GenePosition this is:
		   'transcript' 	: "relative to the start of the gene on the
					   Position's map"
		   'coding|exon|intron' : "relative to the start of the default
					   transcript of the gene on the Position's map"
	 Args	 : none to get, OR
		   Bio::Map::GeneRelative to set

   seq
	Title	: seq
	Usage	: my $string = $position->seq();
	Function: Get/set the sequence as a string of letters. If no sequence is
		  manually set by you, the position's map will be asked for the
		  sequence, and if available, that will be returned.
	Returns : scalar
	Args	: Optionally on set the new value (a string). An optional second
		  argument presets the alphabet (otherwise it will be guessed).

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