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::*