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

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

	   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

       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.

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AUTHOR - Sendu Bala

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

	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

	Title	: map
	Usage	: my $map = $position->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

	Title	: element
	Usage	: my $element =	$position->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

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

	 Title	 : relative
	 Usage	 : my $relative	= $position->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

	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)


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