Bio::Range - Pure perl RangeI implementation
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)
$range = new Bio::Range(-start=>10, -end=>30, -strand=>+1); $r2 = new Bio::Range(-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";
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The rest of the documentation details each of the object methods. Internal metho ds 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 : two of (-start, -end, '-length') - the third is calculated : -strand (defaults to 0)
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 strandidness Example : $st = $range->strand(); $range->strand(-1); Returns : the value of the strandedness (-1, 0 or 1) Args : optionaly, 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, and exeption 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 wether $r1 totaly contains $r2 Args : a range to test for being contained Returns : true if the argument is totaly contained within this range Inherited: Bio::RangeI
Title : equals Usage : if($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 to find the union of Returns : the range containing all of the ranges Inherited: Bio::RangeI::union
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.