Bio::Tools::Primer3Redux::Result
# 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 $rp->seq->seq; }
This is a simple holder class for Primer3 sequence results. The sequence used by default is the one returned in the Primer3 results, but one can pass in a (more-SeqFeature/Annotation-rich) version as a Bio::Seq using attach_seq() (see below for more on this).
This parser will attach any lazily-generated features to that Bio::Seq object. The sequence can be retrieved via get_seq() at any point, such as prior to the end of a parse). To retrieve a sequence guaranteed to have all Primer/PrimerPair data attached, use get_processed_seq(). Switching seqs will cause a new batch of features to be generated and attached.
Please note that primer3 does not terminate on errors during primer design (e.g. due to input parameters that are impossible to fulfill). To check if errors or warnings were produced, it is recommended to always check the result object for errors like so:
if ($result->errors){ # handle the situation }
Bio::Tools::Primer3Redux::Result - Result class for Primer3 data
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Nathan Hillson
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Function: Builds a new Bio::Tools::Primer3::Result object Returns : an instance of Bio::Tools::Primer3::Result Args :
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
Title : get_seq Usage : $obj->get_seq Function : Returns : Args :
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
Title : num_primer_pairs Usage : $obj->num_primer_pairs Function : Returns : Args :
Title : next_left_primer Usage : $obj->next_left_primer Function : Returns : Args :
Title : next_right_primer Usage : $obj->next_right_primer Function : Returns : Args :
Title : next_internal_oligo Usage : $obj->next_internal_oligo Function : Returns : Args :
Title : next_primer_pair Usage : $obj->next_primer_pair Function : Returns : Args :
Title : persistent_data Usage : $obj->persistent_data Function : Returns : Args :
Title : run_parameters Usage : $obj->run_parameters Function : Returns : Args :
Title : run_parameter Usage : $obj->run_parameter('FOO') Function : Returns : Args :
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
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
Title : rewind Usage : $obj->rewind('primer_pair') Function : Returns : Args :
cjfields <cjfields@bioperl.org>
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.
To install Bio::Tools::Primer3Redux, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Tools::Primer3Redux
CPAN shell
perl -MCPAN -e shell install Bio::Tools::Primer3Redux
For more information on module installation, please visit the detailed CPAN module installation guide.