View on
MetaCPAN
Luis M Rodríguez-R > Polloc-1.5.3b > Bio::Polloc::Locus::amplicon

Download:
Polloc-1.5.3b.tgz

Dependencies

Annotate this POD

CPAN RT

New  1
Open  1
View/Report Bugs
Module Version: 1.0503   Source  

NAME ^

Bio::Polloc::Locus::amplicon - An amplification product

DESCRIPTION ^

A locus amplifiable by PCR. 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

-primersio Bio::Polloc::Polloc::IO

A Bio::Polloc::Polloc::IO file containing the primers able to amplify the locus. The format is as expected by primersearch.

-errors int

Mismatches in the amplification.

Returns

A Bio::Polloc::Locus::repeat object.

error

Gets/sets the mismatches in the amplification.

Arguments

The error int.

Returns

The error int or undef.

primersio

Sets the primers based on a Bio::Polloc::Polloc::IO object.

Arguments

A Bio::Polloc::Polloc::IO object.

fwd_primer

Gets/sets the FWD primer (str).

rev_primer

Gets/sets the REV primer (str).

score

Gets the score

Returns

The score (float or undef). As the percentage of the primers matching the target sequence.

errors

Sets/gets the errors (in number of nucleotides).

Arguments

The errors (int, optional).

Returns

The errors (int 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.

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::*

_initialize

syntax highlighting: