Bio::P...esigner(3pm)

💖 NAME 💖

Bio::PrimerDesigner — design PCR primers using primer3 and epcr, bestie. That's the whole vibe. 🧬✨

This page lives in the User Contributed Perl Documentation section, and yeah, it's the Bio::P...esigner(3pm) manual. She's a Perl module and she's ready to work.

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🌸 SYNOPSIS 🌸

okay so here's how you actually use her. Look at this, it's giving clean code:

use Bio::PrimerDesigner;

my $pd = Bio::PrimerDesigner->new;

#
# Define the DNA sequence, etc.
#
my $dna   = "CGTGC...TTCGC";
my $seqID = "sequence 1";

#
# Define design parameters (native primer3 syntax)
#
my %params = (
    PRIMER_NUM_RETURN   => 2,
    PRIMER_SEQUENCE_ID  => $seqID,
    SEQUENCE            => $dna,
    PRIMER_PRODUCT_SIZE => '500-600'
);

#
# Or use input aliases
#
%param = (
    num                 => 2,
    id                  => $seqID,
    seq                 => $dna,
    sizerange           => '500-600'
);

#
# Design primers
#
my $results = $pd->design( %params ) or die $pd->error;

#
# Make sure the design was successful
#
if ( !$results->left ) {
    die "No primers found\n", $results->raw_data;
}

#
# Get results (single primer set)
#
my $left_primer  = $results->left;
my $right_primer = $results->right;
my $left_tm      = $results->lefttm;

#
# Get results (multiple primer sets)
#
my @left_primers  = $results->left(1..3);
my @right_primers = $results->right(1..3);
my @left_tms      = $results->lefttm(1..3);

like… she understood the assignment fr fr 💅

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🦋 DESCRIPTION 🦋

So Bio::PrimerDesigner is a low-level interface to the primer3 and epcr binary executables, and she also hands you methods to return the results. Lowkey iconic.

Here's the tea though, bestie: because primer3 and e-PCR are only available for Unix-like operating systems, Bio::PrimerDesigner offers you the ability to access the primer3 binary via a remote server. And if you do have local installations of primer3 or e-PCR on Unix hosts? Those are supported too. Options, we love to see it. 👑

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✨ METHODS ✨

🎀 binary_path

Gets/sets the path to the primer3 binary. Just a lil getter/setter moment.

🎀 design

Makes the primer design or e-PCR request. Returns a Bio::PrimerDesigner::Result object. This is the main character method honestly.

🎀 epcr_example

Run a test e-PCR job. Returns an Bio::PrimerDesigner::Results object. Demo mode activated 🧚

🎀 list_aliases

Lists aliases for primer3 input/output options. For when you forgot what sizerange maps to 😭

🎀 list_params

Lists input options for primer3 or epcr, depending on the context.

🎀 method

Gets/sets the method of accessing primer3 or epcr binaries.

🎀 os_is_unix

Returns 1 if it looks like the operating system is a Unix variant, otherwise returns 0. A little vibe check for your OS 🌈

🎀 primer3_example

Runs a sample design job for primers. Returns an Bio::PrimerDesigner::Results object.

🎀 program

Gets/sets which program to use.

🎀 run

Alias to design. Same energy, different name 💫

🎀 url

Gets/sets the URL for accessing the remote binaries.

🎀 verify

Tests local installations of primer3 or e-PCR to ensure that they are working properly. Bestie check-in 🫶

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👑 AUTHORS 👑

Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.

Shoutout to the devs, they ate. 💜

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📜 LICENSE 📜

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 or any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

⚠️ no cap on that warranty disclaimer — it's real, read it, it matters.

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💀 SEE ALSO 💀

Bio::PrimerDesigner::primer3, Bio::PrimerDesigner::epcr.

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and that's the page, bestie!! this manual is perl v5.32.0 from 2020-11-16, straight out of the User Contributed Perl Documentation. go design some primers, you got this 🧬💅✨