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Bio::Map::GeneRelativeUser Contributed Perl DocumentaBio::Map::GeneRelative(3)

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://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 $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 v5.24.1			  2017-07-08	     Bio::Map::GeneRelative(3)

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

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