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Bio-Tools-Primer3Redux-0.04
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/ Bio::Tools::Primer3Redux::Result

NAME

Bio::Tools::Primer3Redux::Result

SYNOPSIS

# parse a Primer3 report, and get Bio::Tools::Primer3Redux::Result
while (my $result = $parser->next_result) {
    (say "primer design failed" and next) if $result->errors;

    say $result->num_primer_pairs;
    my $pair = $result->next_primer_pair;

    my ($fp, $rp) = ($pair->forward_primer, $pair->reverse_primer);

    say $fp->seq->seq;
    say $rp->seq->seq;
}

DESCRIPTION

This is a simple holder class for Primer3 sequence results. The sequence used by default is the one returned in the Primer3 results, but one can pass in a (more-SeqFeature/Annotation-rich) version as a Bio::Seq using attach_seq() (see below for more on this).

This parser will attach any lazily-generated features to that Bio::Seq object. The sequence can be retrieved via get_seq() at any point, such as prior to the end of a parse). To retrieve a sequence guaranteed to have all Primer/PrimerPair data attached, use get_processed_seq(). Switching seqs will cause a new batch of features to be generated and attached.

Please note that primer3 does not terminate on errors during primer design (e.g. due to input parameters that are impossible to fulfill). To check if errors or warnings were produced, it is recommended to always check the result object for errors like so:

if ($result->errors){
  # handle the situation
}

NAME

Bio::Tools::Primer3Redux::Result - Result class for Primer3 data

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR - Chris Fields

Email cjfields at bioperl dot org

Describe contact details here

CONTRIBUTORS

Nathan Hillson

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $obj = new
Function: Builds a new Bio::Tools::Primer3::Result object
Returns : an instance of Bio::Tools::Primer3::Result
Args    :

attach_seq

Title    : attach_seq
Usage    : $obj->attach_seq
Function :
Returns  : Bio::SeqI
Args     : Bio::SeqI (warning: may or may not have primers attached)
Note     : calling this method resets the feature iterators to prevent (for
           instance) issues with references

get_seq

Title    : get_seq
Usage    : $obj->get_seq
Function :
Returns  :
Args     :

get_processed_seq

Title    : get_processed_seq
Usage    : $obj->get_processed_seq
Function :
Returns  :
Args     :
Note     : unlike get_seq(), this guarantees getting back the full
           sequence with attached Primer/PrimerPair SeqFeatureI

num_primer_pairs

Title    : num_primer_pairs
Usage    : $obj->num_primer_pairs
Function :
Returns  :
Args     :

next_left_primer

Title    : next_left_primer
Usage    : $obj->next_left_primer
Function :
Returns  :
Args     :

next_right_primer

Title    : next_right_primer
Usage    : $obj->next_right_primer
Function :
Returns  :
Args     :

next_internal_oligo

Title    : next_internal_oligo
Usage    : $obj->next_internal_oligo
Function :
Returns  :
Args     :

next_primer_pair

Title    : next_primer_pair
Usage    : $obj->next_primer_pair
Function :
Returns  :
Args     :

persistent_data

Title    : persistent_data
Usage    : $obj->persistent_data
Function :
Returns  :
Args     :

run_parameters

Title    : run_parameters
Usage    : $obj->run_parameters
Function :
Returns  :
Args     :

run_parameter

Title    : run_parameter
Usage    : $obj->run_parameter('FOO')
Function :
Returns  :
Args     :

warnings

Title   : warnings
Function: returns a list of the warning messages returned by primer3, if any
Usage   : my @warnings = $obj->warnings;
Args    : none
Returns : Array of messages

errors

Title   : errors
Function: returns a list of the error messages returned by primer3, if any
Usage   : my @errors = $obj->errors;
Args    : none
Returns : Array of messages

rewind

Title    : rewind
Usage    : $obj->rewind('primer_pair')
Function :
Returns  :
Args     :

AUTHOR

cjfields <cjfields@bioperl.org>

COPYRIGHT AND LICENSE

This software is copyright (c) 2011 by Chris Fields.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.