Bio::T...rimer3(3pm)

💖 Bio::T...rimer3 💖

okay bestie, gather round, because we're talking about Bio::Tools::Run::Primer3 from the User Contributed Perl Documentation collection — yes, that's the manual we're living in rn. It's a Perl module that makes input for and works with the output from the program primer3. primer3 does the primer design, this module does the ✨talking to it✨ part. slay.

---

🌸 NAME 🌸

Bio::Tools::Run::Primer3 — Create input for and work with the output from the program primer3. that's the whole vibe, periodt.

---

✨ SYNOPSIS ✨

Bio::Tools::Primer3 creates the input files you need to design primers using primer3, and it also gives you the mechanisms to access data in the primer3 output files. two jobs, both ate.

This module is a bioperl interface to the program primer3. See http://frodo.wi.mit.edu/primer3/primer3_code.html for details and to download the software. Heads up bestie: this module only works for primer3 release 1 but is not guaranteed to work with earlier versions. no cap, read that twice.

# 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. (yes I'm saying it again, it's that important 💅)

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). Our author ripped some of his code and added a lot of their own. Their exact words: "I hope he is not mad at me!" 😭 we love a humble king.

---

🫶 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, fr fr.

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. the reason? 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 — the more context, the more slay.

🐛 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://redmine.open-bio.org/projects/bioperl/

---

👑 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 _ — that's your lil secret handshake, iykyk.

---

💫 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. 🙈 (author's words, not mine)
• 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. 📚

---

💫 version

• Title — version
• Usage — $v = $prog->version();
• Function — Determine the version number of the program
• Example —
• Returns — float or undef
• Args — none

---

💫 _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. 📚

---

and that's the whole page bestie!! 🎀 this gorgeous thing ships with perl v5.36.0, dated 2023-01-22, and it lives under the Bio::T...rimer3(3pm) manual name — go forth and design some primers, you absolute icon 💅✨🧬