bio::coordinate::extrapolatingpair(3pm) [debian man page]
Bio::Coordinate::ExtrapolatingPair(3pm) User Contributed Perl Documentation Bio::Coordinate::ExtrapolatingPair(3pm) NAME
Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets SYNOPSIS
use Bio::Location::Simple; use Bio::Coordinate::ExtrapolatingPair; $match1 = Bio::Location::Simple->new (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 ); $match2 = Bio::Location::Simple->new (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 ); $pair = Bio::Coordinate::ExtrapolatingPair-> new(-in => $match1, -out => $match2, -strict => 1 ); $pos = Bio::Location::Simple->new (-start => 40, -end => 60, -strand=> 1 ); $res = $pair->map($pos); $res->start eq 20; $res->end eq 20; DESCRIPTION
This class represents a one continuous match between two coordinate systems represented by Bio::Location::Simple objects. The relationship is directed and reversible. It implements methods to ensure internal consistency, and map continuous and split locations from one coordinate system to another. This class is an elaboration of Bio::Coordinate::Pair. The map function returns only matches which is the mode needed most of tehtime. By default the matching regions between coordinate systems are boundless, so that you can say e.g. that gene starts from here in the chromosomal coordinate system and extends indefinetely in both directions. If you want to define the matching regions exactly, you can do that and set strict() to true. 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: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ strict Title : strict Usage : $obj->strict(1); Function: Set and read the strictness of the coordinate system. Example : Returns : value of input system Args : boolean map Title : map Usage : $newpos = $obj->map($loc); Function: Map the location from the input coordinate system to a new value in the output coordinate system. In extrapolating coodinate system there is no location zero. Locations are... Example : Returns : new location in the output coordinate system or undef Args : Bio::Location::Simple _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 perl v5.14.2 2012-03-02 Bio::Coordinate::ExtrapolatingPair(3pm)
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Bio::Coordinate::Collection(3pm) User Contributed Perl Documentation Bio::Coordinate::Collection(3pm) 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: https://redmine.open-bio.org/projects/bioperl/ 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 perl v5.14.2 2012-03-02 Bio::Coordinate::Collection(3pm)