Luis M Rodríguez-R
and 1 contributors

NAME

Bio::Polloc::Locus::repeat - A repetitive locus

DESCRIPTION

A repeatitive locus. Implements Bio::Polloc::LocusI.

AUTHOR - Luis M. Rodriguez-R

Email lmrodriguezr at gmail dot com

APPENDIX

Methods provided by the package

new

Creates a Bio::Polloc::Locus::repeat object.

Arguments

-period float

The period of the repeat (units length).

-exponent float

The exponent (No of units).

-error float

Mismatches percentage.

-repeats str

Repetitive sequences, repeats space-separated.

-consensus str

Repeats consensus.

Returns

A Bio::Polloc::Locus::repeat object.

period

Gets/sets the period of the repeat. I.e., the size of each repeat.

Arguments

The period (int, optional).

Returns

The period (int or undef)

exponent

Gets/sets the exponent of the repeat. I.e., the number of times the repeat is repeated.

Arguments

The exponent (int, optional).

Returns

The exponent (int or undef).

repeats

Sets/gets the repetitive sequence (each repeat separated by spaces).

Arguments

The repetitive sequence (str, optional).

Returns

The repetitive sequence (str or undef).

consensus

Sets/gets the consensus repeat.

Arguments

The consensus sequence (str, optional).

Returns

The consensus sequence (str or undef).

error

Gets/sets the error rate of the repeat. I.e., the percentage of mismatches.

Arguments

The error (float).

Returns

The error (float or undef).

score

Gets/sets the score

Arguments

The score (float, optional).

Returns

The score (float or undef).

distance

Returns the difference in length with the given locus.

Arguments

-locus Bio::Polloc::LocusI object

The locus to compare with.

-locusref Bio::Polloc::LocusI object

The reference locus. If set, replaces the current loaded object.

-units bool (int)

If true, returns the difference in the number of repeat units, not in base pairs. This flag requires the loci to be Bio::Polloc::Locus::repeat objects.

Returns

Float, the difference in length.

Throws

Bio::Polloc::Polloc::Error if no locus or the loci are not of the proper type.

INTERNAL METHODS

Methods intended to be used only within the scope of Bio::Polloc::*

_initialize