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Bio::Coordinate::ColleUsernContributed Perl DocuBio::Coordinate::Collection(3)

NAME
       Bio::Coordinate::Collection - Noncontinuous match between two
       coordinate sets.

VERSION
       version 1.007001

SYNOPSIS
	 # create Bio::Coordinate::Pairs or other Bio::Coordinate::MapperIs somehow
	 $pair1; $pair2;

	 # add them into a Collection
	 $collection = Bio::Coordinate::Collection->new;
	 $collection->add_mapper($pair1);
	 $collection->add_mapper($pair2);

	 # create a position and map it
	 $pos =	Bio::Location::Simple->new (-start => 5, -end => 9 );
	 $res =	$collection->map($pos);
	 $res->match->start == 1;
	 $res->match->end == 5;

	 # if mapping is many to one (*>1) or many-to-many (*>*)
	 # you have to give seq_id not get unrelevant entries
	 $pos =	Bio::Location::Simple->new
	     (-start =>	5, -end	=> 9 -seq_id=>'clone1');

DESCRIPTION
       Generic,	context	neutral	mapper to provide coordinate transforms
       between two disjoint coordinate systems.	It brings into Bioperl the
       functionality from Ewan Birney's	Bio::EnsEMBL::Mapper ported into
       current bioperl.

       This class is aimed for representing mapping between whole chromosomes
       and contigs, or between contigs and clones, or between sequencing reads
       and assembly. The submaps are automatically sorted, so they can be
       added in	any order.

       To map coordinates to the other direction, you have to swap() the
       collection. Keeping track of the	direction and ID restrictions are left
       to the calling code.

ATTRIBUTES
   mappers
	Title	: mappers
	Usage	: $obj->mappers();
	Function: Returns or sets a list of mappers.
	Example	:
	Returns	: array	of mappers
	Args	: array	of mappers

   each_mapper
	Title	: each_mapper
	Usage	: $obj->each_mapper();
	Function: Returns a list of mappers.
	Example	:
	Returns	: list of mappers
	Args	: none

   mapper_count
	Title	: mapper_count
	Usage	: my $count = $collection->mapper_count;
	Function: Get the count	of the number of mappers stored
		  in this collection
	Example	:
	Returns	: integer
	Args	: none

METHODS
   new
   add_mapper
	Title	: add_mapper
	Usage	: $obj->add_mapper($mapper)
	Function: Pushes one Bio::Coordinate::MapperI into the list of mappers.
		  Sets _is_sorted() to false.
	Example	:
	Returns	: 1 when succeeds, 0 for failure.
	Args	: mapper object

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

   test
	Title	: test
	Usage	: $obj->test;
	Function: test that both components of all pairs are of	the same length.
		  Ran automatically.
	Example	:
	Returns	: boolean
	Args	:

   map
	Title	: map
	Usage	: $newpos = $obj->map($pos);
	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 coordinate system
	Args	: integer

   sort
	Title	: sort
	Usage	: $obj->sort;
	Function: Sort function	so that	all mappings are sorted	by
		  input	coordinate start
	Example	:
	Returns	: 1
	Args	:

INTERNAL METHODS
   _map
	Title	: _map
	Usage	: $newpos = $obj->_map($simpleloc);
	Function: Internal method that does the	actual mapping.	Called multiple	times
		  by map() if the location  to be mapped is a split location

	Example	:
	Returns	: new location in the output coordinate	system or undef
	Args	: Bio::Location::Simple

   _is_sorted
	Title	: _is_sorted
	Usage	: $newpos = $obj->_is_sorted;
	Function: toggle for whether the (internal) coodinate mapper data are sorted
	Example	:
	Returns	: boolean
	Args	: boolean

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::Collection(3)

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

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