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

NAME

Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets.

VERSION

version 1.007001

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.

METHODS

new

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 coordinate system there is no location zero.
           Locations are...
 Example :
 Returns : new location in the output coordinate system or undef
 Args    : Bio::Location::Simple

INTERNAL METHODS

_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

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>

COPYRIGHT

This software is copyright (c) by Heikki Lehvaslaiho.

This software is available under the same terms as the perl 5 programming language system itself.

2020-11-24 perl v5.32.0