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Bio::Tools::Primer3.3pm

NAME

Bio::Tools::Primer3 - Create input for and work with the output from the program primer3

SYNOPSIS

  # parse primer3 output to get some data
  # this is also called from Bio::Tools::Run::Primer3
  use Bio::Tools::Primer3;
 
  # read a primer3 output file
  my $p3 = Bio::Tools::Primer3->new(-file=>"data/primer3_output.txt");
 
  # how many results were there?
  my $num = $p3->number_of_results;
  print "There were $num results\n";
 
  # get all the results
  my $all_results = $p3->all_results;
  print "ALL the results\n";
  foreach my $key (keys %{$all_results}) {
     print "$key\t${$all_results}{$key}\n";
  }
 
  # get specific results
  my $result1 = $p3->primer_results(1);
  print "The first primer is\n";
  foreach my $key (keys %{$result1}) {
     print "$key\t${$result1}{$key}\n";
  }
 
  # get the results as a Bio::Seq::PrimedSeq stream
  my $primer = $p3->next_primer;
  print "The left primer in the stream is ",
    $primer->get_primer('-left_primer')->seq->seq, "\n";
 
 

DESCRIPTION

Bio::Tools::Primer3 creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3 output files.

This module provides a bioperl interface to the program primer3. See http://www-genome.wi.mit.edu/genome_software/other/primer3.html for details and to download the software.

This module is based on one written by Chad Matsalla (bioinformatics1@dieselwurks.com)

I have ripped some of his code, and added a lot of my own. I hope he is not mad at me!

This is probably best run in one of the two following ways:

   i. To parse the output from Bio::Tools::Run::Primer3.
      You will most likely just use next_primer to get the results from
      Bio::Tools::Run::Primer3.
   ii. To parse the output of primer3 handed to it as a file name.
 
 

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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:

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

AUTHOR -

   Rob Edwards
 
   redwards@utmem.edu
 
   Based heavily on work of
 
   Chad Matsalla
 
   bioinformatics1@dieselwurks.com
 
 

CONTRIBUTORS

   Brian Osborne bosborne at alum.mit.edu
 
 

APPENDIX

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

new

   Title   : new()
   Usage   : my $primer3 = Bio::Tools::Primer3->new(-file=>$file)
             to read a primer3 output file.
   Function: Parse primer3 output
   Returns : Does not return anything. If called with a filename will
             allow you to retrieve the results
   Args    : -file (optional) file of primer3 results to parse -verbose
             (optional) set verbose output
   Notes   :
 
 

number_of_results

   Title   : number_of_results()
   Usage   : $primer3->number_of_results()
   Function: Retrieve the number of primers returned from Primer3.
   Returns : A scalar
   Args    : None
   Notes   : This returns the count of the primers returned by Primer3
              (aka how many of them there are).
              This is one more than the maximum offset into the zero
              based list of primers that is accessed by primer_results().
 
 

all_results

   Title   : all_results()
   Usage   : $primer3->all_results() to print all results or
             $primer3->all_results('primer3 result name',
             'other results') to return a specific result
   Function: Retrieve the results returned from Primer3.
   Returns : A reference to a hash
   Args    : Optional array of results to retrieve
 
 

primer_results

   Title   : primer_results()
   Usage   : $primer3->primer_results(2) to print results for the third
             choice primer (indexed on 0)
   Function: Retrieve the results returned from Primer3 for specific primer pairs.
   Returns : A reference to a hash
   Args    : A number between 0 and the maximum number of primers to retrieve
 
 

_readfile

   Title   : _readfile()
   Usage   : $self->_readfile();
   Function: An internal function that reads a file and sets up the results
   Returns : Nothing.
   Args    : None
   Notes   :
 
 

next_primer

   Title   : next_primer()
   Usage   : while (my $primed_seq  = $primer3->next_primer()) {
   Function: Retrieve the primed sequence and a primer pair, one at a time
   Returns : Returns a Bio::Seq::PrimedSeq feature, one at a time
   Args    : None
   Notes   : Use $primed_seq->annotated_seq to get an annotated sequence
             object you can write out.
 
 

primer_stream

   Title   : primer_stream()
   Usage   : while (my $primed_seq  = $primer3->primer_stream()) {
   Function: Retrieve the primer/sequences one at a time
   Returns : Returns a Bio::Seq::PrimedSeq feature, one at a time
   Args    : None
   Notes   : Deprecated, just a link to next_primer
 
 

_separate

   Title   : _separate()
   Usage   : $self->_separate();
   Function: An internal function that groups the results by number
             (e.g. primer pair 1, etc)
   Returns : Nothing.
   Args    : None
   Notes   :
 
 

_set_variable

   Title   : _set_variable()
   Usage   : $self->_set_variable('variable name', 'value');
   Function: An internal function that sets a variable
   Returns : Nothing.
   Args    : None
   Notes   : Used to set $self->{results} and $self->seqobject