NAME

Bio::Polloc::Typing::bandingPattern - banding-pattern-based methods for typing assessment

DESCRIPTION

Category 1 of genotyping methods in:

  Li, W., Raoult, D., & Fournier, P.-E. (2009).
  Bacterial strain typing in the genomic era.
  FEMS Microbiology Reviews, 33(5), 892-916.

AUTHOR - Luis M. Rodriguez-R

Email lmrodriguezr at gmail dot com

APPENDIX

Methods provided by the package

new

Generic initialization method

METHODS FROM Bio::Polloc::TypingI

scan

See Bio::Polloc::TypingI->scan.

fragments must be implemented by the Bio::Polloc::Typing::bandingPattern::* object.

cluster

typing_value

See Bio::Polloc::TypingI->typing_value.

Returns the size of the loci between the minimum (min_size) and the maximum (max_size) size.

Returns

A reference to an array of integers.

graph_content

Generates the expected gel. See Bio::Polloc::TypingI->graph.

SPECIFIC METHODS

fragments

Generates fragments.

Arguments

-locigroup Bio::Polloc::LociGroup

The group of loci to be used as base to design the protocol.

Returns

A Bio::Polloc::LociGrop, where each locus is a fragment.

Throws

A Bio::Polloc::Polloc::NotImplementedException unless implemented by the specific Bio::Polloc::Typing::bandingPattern::* object.

max_size

Gets/sets the maximum locus size. No limit (inf) by default.

min_size

Gets/sets the minimum locus size. 1 by default.

INTERNAL METHODS

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

_initialize

_initialize_method

cpanm Bio::Polloc

perl -MCPAN -e shell
install Bio::Polloc