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Bio::Coordinate::GeneMUserrContributed Perl DocuBio::Coordinate::GeneMapper(3)

NAME
       Bio::Coordinate::GeneMapper - Transformations between gene related
       coordinate systems.

VERSION
       version 1.007001

SYNOPSIS
	 use Bio::Coordinate::GeneMapper;

	 # get a Bio::RangeI representing the start, end and strand of the CDS
	 # in chromosomal (or entry) coordinates
	 my $cds;

	 # get a Bio::Location::Split or an array of Bio::LocationI objects
	 # holding the start, end and strand of	all the	exons in chromosomal
	 # (or entry) coordinates
	 my $exons;

	 # create a gene mapper	and set	it to map from chromosomal to cds coordinates
	 my $gene = Bio::Coordinate::GeneMapper->new(-in   =>'chr',
						     -out  =>'cds',
						     -cds  =>$cds,
						     -exons=>$exons
						    );

	 # get a a Bio::Location or sequence feature in	input (chr) coordinates
	 my $loc;

	 # map the location into output	coordinates and	get a new location object
	 $newloc = $gene->map($loc);

DESCRIPTION
       Bio::Coordinate::GeneMapper is a	module for simplifying the mappings of
       coodinate locations between various gene	related	locations in human
       genetics. It also adds a	special	human genetics twist to	coordinate
       systems by making it possible to	disable	the use	of zero	(0). Locations
       before position one start from -1. See method nozero.

       It understands by name the following coordinate systems and mapping
       between them:

				 peptide (peptide length)
				    ^
				    | -peptide_offset
				    |
			   frame  propeptide (propeptide length)
			       ^    ^
				\   |
		    translate	 \  |
				  \ |
				   cds	(transcript start and end)
				    ^
	     negative_intron	    | \
		     ^		    |  \  transcribe
		      \		    |	\
		     intron	   exon	 \
		      ^	  ^	    ^	  /
	     splice    \   \	  / |	 /
			\   \	 /  |	/
			 \   inex   |  /
			  \    ^    | /
			   \	\   |/
			    ----- gene (gene_length)
				    ^
				    | -	gene_offset
				    |
				   chr (or entry)

       This structure is kept in the global variable $DAG which	is a
       representation of a Directed Acyclic Graph. The path calculations
       traversing this graph are done in a helper class. See
       Bio::Coordinate::Graph.

       Of these, two operations	are special cases, translate and splice.
       Translating and reverse translating are implemented as internal methods
       that do the simple 1<->3	conversion. Splicing needs additional
       information that	is provided by method exons which takes	in an array of
       Bio::LocationI objects.

       Most of the coordinate system names should be selfexplanatory to	anyone
       familiar	with genes. Negative intron coordinate system is starts
       counting	backwards from -1 as the last nucleotide in the	intron.	This
       used when only exon and a few flanking intron nucleotides are known.

       This class models coordinates within one	transcript of a	gene, so to
       tackle multiple transcripts you need several instances of the class. It
       is therefore valid to argue that	the name of the	class should be
       TranscriptMapper. GeneMapper is a catchier name,	so it stuck.

ATTRIBUTES
   nozero
	Title	: nozero
	Usage	: $obj->nozero(1);
	Function: Flag to disable the use of zero in the input,
		  output or both coordinate systems. Use of coordinate
		  systems without zero is a peculiarity	 common	in
		  human	genetics community.
	Example	:
	Returns	: 0 (default), or 'in',	'out', 'in&out'
	Args	: 0 (default), or 'in',	'out', 'in&out'

METHODS
   new
   in
	Title	: in
	Usage	: $obj->in('peptide');
	Function: Set and read the input coordinate system.
	Example	:
	Returns	: value	of input system
	Args	: new value (optional)

   out
	Title	: out
	Usage	: $obj->out('peptide');
	Function: Set and read the output coordinate system.
	Example	:
	Returns	: value	of output system
	Args	: new value (optional)

   strict
	Title	: strict
	Usage	: $obj->strict('peptide');
	Function: Set and read whether strict boundaried of coordinate
		  systems are enforced.
		  When strict is on, the end of	the coordinate range must be defined.
	Example	:
	Returns	: boolean
	Args	: boolean (optional)

   graph
	Title	: graph
	Usage	: $obj->graph($new_graph);
	Function: Set and read the graph object	representing relationships
		  between coordinate systems
	Example	:
	Returns	: Bio::Coordinate::Graph object
	Args	: new Bio::Coordinate::Graph object (optional)

   peptide
	Title	: peptide
	Usage	: $obj->peptide_offset($peptide_coord);
	Function: Read and write the offset of peptide from the	start of propeptide
		  and peptide length
	Returns	: a Bio::Location::Simple object
	Args	: a Bio::LocationI object

   peptide_offset
	Title	: peptide_offset
	Usage	: $obj->peptide_offset(20);
	Function: Set and read the offset of peptide from the start of propeptide
	Returns	: set value or 0
	Args	: new value (optional)

   peptide_length
	Title	: peptide_length
	Usage	: $obj->peptide_length(20);
	Function: Set and read the offset of peptide from the start of propeptide
	Returns	: set value or 0
	Args	: new value (optional)

   exons
	Title	: exons
	Usage	: $obj->exons(@exons);
	Function: Set and read the offset of CDS from the start	of transcript
		  You do not have to sort the exons before calling this	method as
		  they will be sorted automatically.
		  If you have not defined the CDS, is will be set to span all
		  exons	here.
	Returns	: array	of Bio::LocationI exons	in genome coordinates or 0
	Args	: array	of Bio::LocationI exons	in genome (or entry) coordinates

   cds
	Title	: cds
	Usage	: $obj->cds(20);
	Function: Set and read the offset of CDS from the start	of transcipt

		  Simple input can be an integer which gives the start of the
		  coding region	in genomic coordinate. If you want to provide
		  the end of the coding	region or indicate the use of the
		  opposite strand, you have to pass a Bio::RangeI
		  (e.g.	Bio::Location::Simple or Bio::SegFeature::Generic)
		  object to this method.

	Returns	: set value or 0
	Args	: new value (optional)

   map
	Title	: map
	Usage	: $newpos = $obj->map(5);
	Function: Map the location from	the input coordinate system
		  to a new value in the	output coordinate system.
	Example	:
	Returns	: new value in the output coordiante system
	Args	: a Bio::Location::Simple

   direction
	Title	: direction
	Usage	: $obj->direction('peptide');
	Function: Read-only method for the direction of	mapping	deduced	from
		  predefined input and output coordinate names.
	Example	:
	Returns	: 1 or -1, mapping direction
	Args	: new value (optional)

   swap
	Title	: swap
	Usage	: $obj->swap;
	Function: Swap the direction of	transformation
		  (input <-> output)
	Example	:
	Returns	: 1
	Args	:

   to_string
	Title	: to_string
	Usage	: $newpos = $obj->to_string(5);
	Function: Dump the internal mapper values into a human readable	format
	Example	:
	Returns	: string
	Args	:

INTERNAL METHODS
   _clone_loc
	Title	: _clone_loc
	Usage	: $copy_of_loc = $obj->_clone_loc($loc);
	Function: Make a deep copy of a	simple location
	Returns	: a Bio::Location::Simple object
	Args	: a Bio::Location::Simple object to be cloned

   _mapper_code2string
   _mapper_string2code
   _create_pair
	Title	: _create_pair
	Usage	: $mapper = $obj->_create_pair('chr', 'gene', 0, 2555, 10000, -1);
	Function: Internal helper method to create a mapper between
		  two coordinate systems
	Returns	: a Bio::Coordinate::Pair object
	Args	: string, input	coordinate system name,
		  string, output coordinate system name,
		  boolean, strict mapping
		  positive integer, offset
		  positive integer, length
		  1 || -1 , strand

   _translate
	Title	: _translate
	Usage	: $newpos = $obj->_translate($loc);
	Function: Translate the	location from the CDS coordinate system
		  to a new value in the	propeptide coordinate system.
	Example	:
	Returns	: new location
	Args	: a Bio::Location::Simple or Bio::Location::SplitLocationI

   _frame
   _reverse_translate
	Title	: _reverse_translate
	Usage	: $newpos = $obj->_reverse_translate(5);
	Function: Reverse translate the	location from the propeptide
		  coordinate system to a new value in the CSD.
		  Note that a single peptide location expands to cover
		  the codon triplet
	Example	:
	Returns	: new location in the CDS coordinate system
	Args	: a Bio::Location::Simple or Bio::Location::SplitLocationI

   _check_direction
	Title	: _check_direction
	Usage	: $obj->_check_direction();
	Function: Check	and swap when needed the direction the location
		  mapping Pairs	based on input and output values
	Example	:
	Returns	: new location
	Args	: a Bio::Location::Simple

   _get_path
	Title	: _get_path
	Usage	: $obj->_get_path('peptide');
	Function: internal method for finding that shortest path between
		  input	and output coordinate systems.
		  Calculations and caching are handled by the graph class.
		  See L<Bio::Coordinate::Graph>.
	Example	:
	Returns	: array	of the mappers
	Args	: none

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/%%7Bdist%7D

AUTHOR
       Heikki Lehvaslaiho <heikki@bioperl.org>

COPYRIGHT
       This software is	copyright (c) by Heikki	Lehvaslaiho.

       This software is	available under	the same terms as the perl 5
       programming language system itself.

perl v5.32.1			  2016-12-15	Bio::Coordinate::GeneMapper(3)

NAME | VERSION | SYNOPSIS | DESCRIPTION | ATTRIBUTES | METHODS | INTERNAL METHODS | FEEDBACK | AUTHOR | COPYRIGHT

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