Reference

Bio::Range(3pm)

Pure perl RangeI implementation

NAME

Bio::Range - Pure perl RangeI implementation

SYNOPSIS

  $range = Bio::Range->new(-start=>10, -end=>30, -strand=>+1);
  $r2 = Bio::Range->new(-start=>15, -end=>200, -strand=>+1);
  print join(', ', $range->union($r2)), "\n";
  print join(', ', $range->intersection($r2)), "\n";
  print $range->overlaps($r2), "\n";
  print $range->contains($r2), "\n";

DESCRIPTION

This provides a pure perl implementation of the BioPerl range interface.

Ranges are modeled as having (start, end, length, strand). They use Bio-coordinates - all points >= start and <= end are within the range. End is always greater-than or equal-to start, and length is greather than or equal to 1. The behaviour of a range is undefined if ranges with negative numbers or zero are used.

So, in summary:

  length = end - start + 1
  end >= start
  strand = (-1 | 0 | +1)

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 one of the Bioperl mailing lists. Your participation is much appreciated.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

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 _

Constructors

new

  Title   : new
  Usage   : $range = Bio::Range->new(-start => 100, -end=> 200, -strand = +1);
  Function: generates a new Bio::Range
  Returns : a new range
  Args    : -strand (defaults to 0) and any two of (-start, -end, -length),
            the third will be calculated

unions

 Title   : unions
 Usage   : @unions = Bio::Range->unions(@ranges);
 Function: generate a list of non-intersecting Bio::Range objects
           from a list of Bio::Range objects which may intersect
 Returns : a list of Bio::Range objects
 Args    : a list of Bio::Range objects

Member variable access

These methods let you get at and set the member variables

start

  Title    : start
  Function : return or set the start co-ordinate
  Example  : $s = $range->start(); $range->start(7);
  Returns  : the value of the start co-ordinate
  Args     : optionally, the new start co-ordinate
  Overrides: Bio::RangeI::start

end

  Title    : end
  Function : return or set the end co-ordinate
  Example  : $e = $range->end(); $range->end(2000);
  Returns  : the value of the end co-ordinate
  Args     : optionally, the new end co-ordinate
  Overrides: Bio::RangeI::end

strand

  Title    : strand
  Function : return or set the strandedness
  Example  : $st = $range->strand(); $range->strand(-1);
  Returns  : the value of the strandedness (-1, 0 or 1)
  Args     : optionally, the new strand - (-1, 0, 1) or (-, ., +).
  Overrides: Bio::RangeI::strand

length

  Title    : length
  Function : returns the length of this range
  Example  : $length = $range->length();
  Returns  : the length of this range, equal to end - start + 1
  Args     : if you attempt to set the length an exception will be thrown
  Overrides: Bio::RangeI::Length

toString

  Title   : toString
  Function: stringifies this range
  Example : print $range->toString(), "\n";
  Returns : a string representation of this range

Boolean Methods

These methods return true or false.

 $range->overlaps($otherRange) && print "Ranges overlap\n";

overlaps

  Title    : overlaps
  Usage    : if($r1->overlaps($r2)) { do stuff }
  Function : tests if $r2 overlaps $r1
  Args     : a range to test for overlap with
  Returns  : true if the ranges overlap, false otherwise
  Inherited: Bio::RangeI

contains

  Title    : contains
  Usage    : if($r1->contains($r2) { do stuff }
  Function : tests whether $r1 totally contains $r2
  Args     : a range to test for being contained
  Returns  : true if the argument is totally contained within this range
  Inherited: Bio::RangeI

equals

  Title    : equals
  Usage    : if($r1->equals($r2))
  Function : test whether $r1 has the same start, end, length as $r2
  Args     : a range to test for equality
  Returns  : true if they are describing the same range
  Inherited: Bio::RangeI

Geometrical methods

These methods do things to the geometry of ranges, and return triplets (start, end, strand) from which new ranges could be built.

intersection

  Title    : intersection
  Usage    : ($start, $stop, $strand) = $r1->intersection($r2)
  Function : gives the range that is contained by both ranges
  Args     : a range to compare this one to
  Returns  : nothing if they do not overlap, or the range that they do overlap
  Inherited: Bio::RangeI::intersection

union

  Title    : union
  Usage    : ($start, $stop, $strand) = $r1->union($r2);
           : ($start, $stop, $strand) = Bio::Range->union(@ranges);
  Function : finds the minimal range that contains all of the ranges
  Args     : a range or list of ranges
  Returns  : the range containing all of the ranges
  Inherited: Bio::RangeI::union

History