NAME
Bio::Polloc::Rule::tandemrepeat - A rule of type tandemrepeat
DESCRIPTION
This rule is similar to Bio::Polloc::Rule::repeat, but employes TRF (Benson 1999, NAR 27(2):573-580) for the repeats calculation.
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 TRF, 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::tandemrepeat objects.
stringify_value
Produces a string with the value of the rule.
value
Arguments
Value (str or hashref or arrayref). The supported keys are:
- -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)
- -match int
-
Matching weight
- -mismatch int
-
Mismatching penalty
- -indels int
-
Indel penalty
- -minscore float
-
Minimum score
- -maxscore float
-
Maximum score
- -minsim float
-
Minimum similarity percent
- -maxsim float
-
Maximum similarity percent
- -pm float
-
Match probability
- -pi float
-
Indel probability
Return
Value (hashref or undef).
INTERNAL METHODS
Methods intended to be used only within the scope of Bio::Polloc::*
_parameters
_executable
Attempts to find the TRF executable.