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

💖 Bio::P...:Result — the manual page, bestie edition 💖

User Contributed Perl Documentation · Bio::P...:Result(3pm)

okay so you found the Bio::PrimerDesigner::Result page?? slay. this is the class that handles your primer design and validation results, and honestly? it's giving "quiet overachiever." let's get into it 🫶

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✨ NAME ✨

Bio::PrimerDesigner::Result — a whole class dedicated to handling primer design or validation results. she holds the receipts. 💅

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🌸 SYNOPSIS 🌸

use Bio::PrimerDesigner;

#
# primer3
#
my $primer3_obj = Bio::PrimerDesigner->new( program => 'primer3 );
my $result = $primer3_obj->design( %hash_of_options );
my $left_primer = $result->left;
my @left_primers = $result->left(1..$num_primers);

#
# e-PCR -- first make a hash of options from primer3 results
# then run e-PCR
#
my $epcr_obj = Bio::PrimerDesigner->new( program => 'primer3 );
my $epcr_result = $epcr_obj->design( %hash_of_options );
my $num_products = $epcr_result->products;

#
# one product
#
my $first_prod_size = $epcr_result->size;
my $first_prod_start = $epcr_result->start;
my $first_prod_stop = $epcr_result->start;

#
# more than one product
#
my @pcr_product_sizes = ();
for (1..$num_products) {
    push @pcr_product_sizes, $epcr_result->size;
}

like look at her go 🏃♀️💨

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🦋 DESCRIPTION 🦋

so Bio::PrimerDesigner::Result will autogenerate result access methods for for Native Boulder IO keys and Bio::PrimerDesigner keys — for primer3, e-PCR, isPcr and ipcress. no cap, she just makes the accessors for you so you don't have to. main character energy fr fr ✨

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👑 METHODS 👑

🎀 keys 🎀

this one handles all the result method calls made through the Bio::PrimerDesigner::Result object. what you get back depends on what you pass in — scalar or list, bestie, it's a whole vibe check:

• nothing passed → returns the scalar value for set 1
• a numeric n → returns the scalar value for set n
• a numeric list 1..n → returns a list with n elements

for reference, the original lays it out like this: text ------------------+------------------------ Args passed | Returns ------------------+------------------------ none scalar value for set 1 numeric n scalar value for set n numeric list 1..n list with n elements

the aliased output methods (they're right below, keep scrolling 💅) return a string when you call them in scalar context, and a list when you call them in list context. the native primer3 (Boulder IO) keys work too. and yeah, there are also e-PCR, isPcr and ipcress specific methods. versatile queen 👑

🌈 Primer3 keys

• left — left primer sequence
• right — right primer sequence
• hyb_oligo — internal oligo sequence
• startleft — left primer 5' sequence coordinate
• startright — right primer 5' sequence coordinate
• tmleft — left primer tm
• tmright — right primer tm
• qual — primer pair penalty (Q value)
• lqual — left primer penalty
• rqual — right primer penalty
• leftgc — left primer % gc
• rightgc — right primer % gc
• lselfany — left primer self-complementarity (any)
• lselfend — left primer self-complementarity (end)
• rselfany — right primer self-complementarity (any)
• rselfend — right primer self-complementarity (end)
• pairanycomp — primer pair complementarity (any)
• pairendcomp — primer pair complementarity (end)
• lendstab — left primer end stability
• rendstab — right primer end stability
• amplicon — amplified PCR product

🍓 Other keys

• products — number of PCR products
• size — product size
• start — product start coordinate
• stop — product stop coordinate
• end — synonymous with stop
• strand — strand of product relative to the ref. sequence (isPCR, ipcress)
• amplicon — returns the PCR product (isPCR only)

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💜 AUTHOR 💜

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

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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. (like, she's free but she's not making any promises, ok?? 🙈)

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.

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🔥 SEE ALSO 🔥

• Bio::PrimerDesigner

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okay that's the whole page, bestie!! 🎀 this one's from the perl v5.32.0 era, dated 2020-11-16, and it lives at Bio::P...:Result(3pm). go forth and design those primers, you've got this 💖✨🦋