Man pages sections > man3 > Bio::Coordinate

Bio::Coordinate - Modules for working with biological coordinates

Bio::Coordinate(3pm) User Contributed Perl Documentation Bio::Coordinate(3pm)

NAME

Bio::Coordinate - Modules for working with biological coordinates

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

Bio::Coordinate classes are used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.

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> This software is copyright (c) by Heikki Lehvaslaiho.
This software is available under the same terms as the perl 5 programming language system itself.
2017-08-30 perl v5.26.0