| Bio::Range(3pm) | User Contributed Perl Documentation | Bio::Range(3pm) |
Bio::Range - Pure perl RangeI implementation
$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";
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)
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.
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Please direct usage questions or support issues to the mailing list:
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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.
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:
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
These methods let you get at and set the member variables
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
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
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
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
Title : toString Function: stringifies this range Example : print $range->toString(), "\n"; Returns : a string representation of this range
These methods return true or false.
$range->overlaps($otherRange) && print "Ranges overlap\n";
Title : overlaps
Usage : if($r1->overlaps($r2)) { do stuff }
Function : tests if $r2 overlaps $r1
Args : a range to test for overlap with
Returns : true if the ranges overlap, false otherwise
Inherited: Bio::RangeI
Title : contains
Usage : if($r1->contains($r2) { do stuff }
Function : tests whether $r1 totally contains $r2
Args : a range to test for being contained
Returns : true if the argument is totally contained within this range
Inherited: Bio::RangeI
Title : equals Usage : if($r1->equals($r2)) Function : test whether $r1 has the same start, end, length as $r2 Args : a range to test for equality Returns : true if they are describing the same range Inherited: Bio::RangeI
These methods do things to the geometry of ranges, and return triplets (start, end, strand) from which new ranges could be built.
Title : intersection Usage : ($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
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
| 2020-10-28 | perl v5.30.3 |