Bio::Polloc::Rule::repeat - A rule of type repeat
Email lmrodriguezr at gmail dot com
Methods provided by the package
Generic initialization method
This is where magic happens. Translates the parameters of the object into a call to mreps, and scans the sequence for repeats.
The sequence (-seq) as a Bio::Seq or a Bio::SeqIO object
-seq
An array reference populated with Bio::Polloc::Locus::repeat objects
Produces a readable string containing the value of the rule.
Implements the _qualify_value() from the Bio::Polloc::RuleI interface
_qualify_value()
Value (str or ref-to-hash or ref-to-array). The supported keys are:
Resolution (allowed error)
Minimum size of the repeat
Maximum size of the repeat
Minimum period of the repeat
Maximum period of the repeat
Minimum exponent (number of repeats)
If true, allows spurious results
Process by sliding windows of size 2*n overlaping by n
2*n
n
Minimum similarity percent
Maximum similarity percent
Value (hashref or undef).
undef
Methods intended to be used only within the scope of Bio::Polloc::*
Attempts to calculate the consensus of the repeat units.
The repetitive sequence with repeat units separated by spaces (str).
The consensus sequence (str)
Attempts to get the mreps executable.
To install Bio::Polloc::RuleI, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Polloc::RuleI
CPAN shell
perl -MCPAN -e shell install Bio::Polloc::RuleI
For more information on module installation, please visit the detailed CPAN module installation guide.