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

💖 Bio::P...:ispcr(3pm) 💖

okay bestie, gather round, because this is the Bio::PrimerDesigner::ispcr page and it's literally the little gremlin that talks to isPcr for you 🧚✨

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✨ NAME ✨

Bio::PrimerDesigner::ispcr — a whole class for accessing the isPcr (in-silico PCR) binary 🧬💅

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🌸 SYNOPSIS 🌸

use Bio::PrimerDesigner::ispcr;

that's it. that's the whole vibe. 💜

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🦋 DESCRIPTION 🦋

so this is a low-level interface to the isPcr program, no cap. you hand it your supplied PCR primers, your DNA sequence, and your stringency parameters, and it goes off and predicts both the expected AND the unexpected PCR products. yes, both. it's giving overachiever and we love that for it 🔥

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🎀 METHODS 🎀

🌟 run

sets up the isPcr request for a single primer combination and returns a Bio::PrimerDesigner::Result object 🫶

if the permute flag is true, then all three possible primer combinations get tested, like:

• forward + reverse
• forward + forward
• reverse + reverse

all of them. every single one. it's thorough 💅

🌟 request

assembles the config file and the command-line arguments, then sends the request off to either the local binary or the remote server 📨✨

🌟 verify

this one checks that the isPCR binary is actually installed and actually functioning properly, and it matters more than you'd think bestie 😭

here's the tea: since ispcr returns nothing if no PCR product is found in the sequence, we literally have to be able to tell the difference between:

• a valid, undefined output coming from a working ispcr, and
• an undefined output for some other reason entirely 💀

so verify uses sham ispcr data that is known to produce a PCR product. icon behaviour honestly 👑

🌟 binary_name

defines the binary's name on the system 🌈

🌟 list_aliases

there are no aliases to list for ispcr. nothing. zero. the void 🕳️ (it's fine, we still love it)

🌟 list_params

returns a list of ispcr configuration options 📋

required ispcr input is:

• a sequence string or file
• the left and right primers

and for all the remaining options? default values get used if none are supplied. easy. periodt 💅✨

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👑 AUTHOR 👑

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

shoutout to the 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. 🏛️

not me reading the warranty disclaimer like it's a horror story 💀 no warranty bestie, you're on your own, proceed with caution 🫶

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🌈 SEE ALSO 🌈

• Bio::PrimerDesigner::primer3 — the sibling, the other one, go read it too 💖

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and that's the whole page!! you ate that fr fr ✨

this little gem is Bio::P...:ispcr(3pm), shipped with perl v5.32.0 and dated 2020-11-16 — courtesy of the User Contributed Perl Documentation crew 🎀 thanks for coming to my ted talk, ily, go write some primers 💅🧬💖