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.

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://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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq