Christopher Fields > Bio-Tools-Primer3Redux-0.09 > Bio::Tools::Primer3Redux::Result

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Module Version: 0.09   Source  

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.

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