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Bio::Tools::Run::Primer3.3pm

NAME

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

SYNOPSIS

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://frodo.wi.mit.edu/primer3/primer3_code.html for details and to download the software. This module should work for primer3 release 1 but is not guaranteed to work with earlier versions.

   # design some primers.
   # the output will be put into temp.out
   use Bio::Tools::Run::Primer3;
   use Bio::SeqIO;
 
   my $seqio = Bio::SeqIO->new(-file=>'data/dna1.fa');
   my $seq = $seqio->next_seq;
   my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq,
                                               -outfile => "temp.out",
                                               -path => "/usr/bin/primer3_core");
 
   # or after the fact you can change the program_name
   $primer3->program_name('my_suprefast_primer3');
 
   unless ($primer3->executable) {
     print STDERR "primer3 can not be found. Is it installed?\n";
     exit(-1)
   }
 
   # what are the arguments, and what do they mean?
   my $args = $primer3->arguments;
 
   print "ARGUMENT\tMEANING\n";
   foreach my $key (keys %{$args}) {print "$key\t", $$args{$key}, "\n"}
 
   # set the maximum and minimum Tm of the primer
   $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
 
   # design the primers. This runs primer3 and returns a 
   # Bio::Tools::Run::Primer3 object with the results
   $results = $primer3->run;
 
   # see the Bio::Tools::Run::Primer3 pod for
   # things that you can get from this. For example:
 
   print "There were ", $results->number_of_results, " primers\n";
 
 

Bio::Tools::Run::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!

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://www.bioperl.org/MailList.html             - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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

Shawn Hoon shawnh-at-stanford.edu Jason Stajich jason-at-bioperl.org Brian Osborne osborne1-at-optonline.net

SEE ALSO

Bio::Tools::Primer3

APPENDIX

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

new()

  Title   : new()
  Usage   : my $primer3 = Bio::Tools::Run::Primer3->new(-file=>$file) to read 
            a primer3 output file.
            my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>sequence object) 
            design primers against sequence
  Function: Start primer3 working and adds a sequence. At the moment it 
            will not clear out the old sequence, but I suppose it should.
  Returns : Does not return anything. If called with a filename will allow 
            you to retrieve the results
  Args    : -seq (optional) Bio::Seq object of sequence. This is required 
            to run primer3 but can be added later with add_targets()
                 -outfile file name to output results to (can also be added 
            with $primer3->outfile_name
                 -path path to primer3 executable, including program name, e.g. 
            "/usr/bin/primer3_core". This can also be set with program_name 
            and program_dir
                 -verbose (optional) set verbose output
  Notes   :
 
 

program_name

  Title   : program_name
  Usage   : $primer3->program_name()
  Function: holds the program name
  Returns:  string
  Args    : None
 
 

program_dir

  Title   : program_dir
  Usage   : $primer3->program_dir($dir)
  Function: returns the program directory, which may also be obtained from ENV variable.
  Returns :  string
  Args    :
 
 

add_targets()

  Title   : add_targets()
  Usage   : $primer3->add_targets(key=>value)
  Function: Add any legal value to the input command line. 
  Returns : Returns the number of arguments added.
  Args    : Use $primer3->arguments to find a list of all the values 
            that are allowed, or see the primer3 docs.
  Notes   : This will only do limited error checking at the moment, 
            but it should work.
 
 

run()

  Title   : run()
  Usage   : $primer3->run();
  Function: Run the primer3 program with the arguments that you have supplied.
  Returns : A Bio::Tools::Primer3 object containing the results.
  Args    : None.
  Note    : See the Bio::Tools::Primer3 documentation for those functions.
 
 

arguments()

  Title   : arguments()
  Usage   : $hashref = $primer3->arguments();
  Function: Describes the options that you can set through Bio::Tools::Run::Primer3, 
            with a brief (one line) description of what they are and their 
            default values
  Returns : A string (if an argument is supplied) or a reference to a hash.
  Args    : If supplied with an argument will return a string of its 
            description.
            If no arguments are supplied, will return all the arguments as a 
            reference to a hash
  Notes   : Much of this is taken from the primer3 README file, and you should 
            read that file for a more detailed description.
 
 

_input_args()

  Title   : _input_args()
  Usage   : an internal method to set the input arguments for Primer3
  Function: Define a hash with keys for each of the input arguments and values 
            as a short one line description
  Returns : A reference to a hash.
  Args    : None.
  Notes   : Much of this is taken from the primer3 README file, and you should 
            read that file for a more detailed description.