Bio::P...r::epcr(3pm)

💖 NAME 💖

Bio::PrimerDesigner::epcr — it's a whole class, and its entire personality is accessing the epcr binary. That's the job. That's the vibe. 👑

This page lives in the User Contributed Perl Documentation, under Bio::PrimerDesigner::epcr(3pm), and it's here to make you besties with the e-PCR binary. 🫶

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✨ SYNOPSIS ✨

use Bio::PrimerDesigner::epcr;

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🦋 DESCRIPTION 🦋

Okay so bestie, listen up. This is a low-level interface to the e-PCR binary. You bring your PCR primers, your DNA sequence, and your stringency parameters, and it goes off and predicts both the expected and the unexpected PCR products. Yes, the surprise ones too. We do not gatekeep results here. 🔥

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💅 METHODS 💅

run

Sets up the e-PCR request for a single primer combination and hands you back a Bio::PrimerDesigner::Result object. Little gift. 🎁

If the permute flag is true, then all three possible primer combinations get tested — that's forward + reverse, forward + forward, and reverse + reverse. Exhaustive. Thorough. Iconic. 💫

request

Assembles the e-PCR config file and the command-line arguments, then sends the whole e-PCR request off to the local e-PCR binary or the remote server. Like a messenger pigeon but for genomics. 🕊️

verify

Checks that the e-PCR binary is installed and functioning properly. And here's the plot twist 😭 — e-PCR returns nothing when no PCR product is found in the sequence, so you can't just look at empty output and shrug. You have to be able to tell the difference between:

• a valid, undefined output coming from a functioning e-PCR, and
• an undefined output that happened for some other reason entirely. 💀

So verify uses sham e-PCR data that is known to produce a PCR product. Fake data, real answers, main character energy. 🎭

binary_name

Defines the binary's name on the system. Short. Sweet. Iconic. ✨

list_aliases

There are no aliases to list for epcr. The list is empty, the vibe is minimalist, and honestly? Respect. 🎀

list_params

Returns a list of e-PCR configuration options. 🧾 Required e-PCR input is a sequence string or file plus the left and right primers. Everything else? If you don't supply it, default values get used for the remaining options. No cap. 🌸

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🌈 AUTHOR 🌈

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

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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.

Seriously bestie, the warranty thing is not a bit — no promises of merchantability or fitness for a particular purpose. Read the actual license. 🙈

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👀 SEE ALSO 👀

Bio::PrimerDesigner::primer3. Go read that one next, it's giving sequel energy. 💖

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That's the whole page, babe. This was Bio::PrimerDesigner::epcr(3pm) from the User Contributed Perl Documentation, generated by perl v5.32.0 on 2020-11-16. Slay, and remember: read your manpages, hydrate, and always verify your binary. 💅🌸