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::*