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Bio::Map::GenePositionUser Contributed Perl DocumentaBio::Map::GenePosition(3)

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

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 v5.24.1			  2017-07-08	     Bio::Map::GenePosition(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sendu Bala | APPENDIX

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