NAME
Bio::Polloc::Rule::repeat - A rule of type repeat
AUTHOR - Luis M. Rodriguez-R
Email lmrodriguezr at gmail dot com
APPENDIX
Methods provided by the package
new
Generic initialization method
execute
This is where magic happens. Translates the parameters of the object into a call to mreps, and scans the sequence for repeats.
Arguments
The sequence (-seq) as a Bio::Seq or a Bio::SeqIO object
Returns
An array reference populated with Bio::Polloc::Locus::repeat objects
stringify_value
Produces a readable string containing the value of the rule.
value
Implements the _qualify_value() from the Bio::Polloc::RuleI interface
Arguments
Value (str or ref-to-hash or ref-to-array). The supported keys are:
- -res float
-
Resolution (allowed error)
- -minsize int
-
Minimum size of the repeat
- -maxsize int
-
Maximum size of the repeat
- -minperiod float
-
Minimum period of the repeat
- -maxperiod float
-
Maximum period of the repeat
- -exp float
-
Minimum exponent (number of repeats)
- -allowsmall bool (int)
-
If true, allows spurious results
- -win float
-
Process by sliding windows of size
2*noverlaping byn - -minsim float
-
Minimum similarity percent
- -maxsim float
-
Maximum similarity percent
Return
Value (hashref or undef).
INTERNAL METHODS
Methods intended to be used only within the scope of Bio::Polloc::*
_calculate_consensus
Attempts to calculate the consensus of the repeat units.
Arguments
The repetitive sequence with repeat units separated by spaces (str).
Returns
The consensus sequence (str)
_parameters
_executable
Attempts to get the mreps executable.