Bio::Coordinate::Collection.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

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.

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 lists 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 the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

CONTRIBUTORS

Ewan Birney, birney@ebi.ac.uk

APPENDIX

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

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
 
 

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
 
 

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
 
 

_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
 
 

sort

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

_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