Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets
# 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');
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.
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
Ewan Birney, firstname.lastname@example.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : mappers Usage : $obj->mappers(); Function: Returns or sets a list of mappers. Example : Returns : array of mappers Args : array of mappers
Title : each_mapper Usage : $obj->each_mapper(); Function: Returns a list of mappers. Example : Returns : list of mappers Args : none
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
Title : swap Usage : $obj->swap; Function: Swap the direction of mapping;input <-> output Example : Returns : 1 Args :
Title : test Usage : $obj->test; Function: test that both components of all pairs are of the same length. Ran automatically. Example : Returns : boolean Args :
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
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
Title : sort Usage : $obj->sort; Function: Sort function so that all mappings are sorted by input coordinate start Example : Returns : 1 Args :
Title : _is_sorted Usage : $newpos = $obj->_is_sorted; Function: toggle for whether the (internal) coodinate mapper data are sorted Example : Returns : boolean Args : boolean