Bio::Coordinate - Modules for working with biological coordinates
# create Bio::Coordinate::Pairs or other Bio::Coordinate::MapperIs somehow
# add them into a Collection
$collection = Bio::Coordinate::Collection->new;
# 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');
Bio::Coordinate classes are used for working with various biological coordinate
systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for
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modules. Send your comments and suggestions preferably to the Bioperl mailing
list. Your participation is much appreciated.
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Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive
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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 of the bugs
and their resolution. Bug reports can be submitted via the web:
Heikki Lehvaslaiho <firstname.lastname@example.org>
This software is copyright (c) by Heikki Lehvaslaiho.
This software is available under the same terms as the perl 5 programming
language system itself.