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

💖 Bio::T...rofile(3pm) 💖

okay bestie, this one lives in the User Contributed Perl Documentation section of your man pages, and it's the whole tea on Bio::Tools::PSort::Profile — the Perl implementation of the Profile protein subcellular localization method. slay. let's get into it 🧚

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✨ NAME ✨

Bio::Tools::PSort::Profile — a Perl implementation of the Profile protein subcellular localization method. it does exactly what it says on the tin, no cap 💅

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🌸 SYNOPSIS 🌸

use Bio::Tools::PSort::Profile;

# Load a previously trained profile from a file.
$motif = new Bio::Tools::PSort::Profile(-database => 'profile-db.txt');

# Attempt to match on a Bio::Seq object.
@matches = $motif->match($seq);
print($seq->display_id . ": matched " . $_->profile_id . "\n") for(@matches);

look at that. load a trained profile from a file, throw a Bio::Seq at it, print the matches. the way that $_->profile_id just works 😭 iconic

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🦋 DESCRIPTION 🦋

Bio::Tools::Motif uses a selection of motifs that have been identified to be typical of proteins resident at a specific subcellular localization.

so here's the vibe: the module takes a Bio::Seq object and tries to match it against a database. if it succeeds, it hands you back one or more Bio::Tools::Motif::Match objects with the prediction information inside. that's the whole plot, and honestly? it ate. 🔥

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🎀 CONSTRUCTOR 🎀

$motif = new Bio::Tools::Motif(-database => 'motif-db.txt');

the Motif constructor accepts the name of an existing database file. that's it, that's the whole job. point it at your file and go 💖

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⭐ METHODS ⭐

@matches = $motif->match($seq);

the match method accepts a Bio::Seq object as an argument and returns an array of Bio::Tools::Motif::Match objects that matched the given sequence. main character method energy fr fr 👑

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🌈 AUTHOR 🌈

Fiona Brinkman, Chris Walsh, Matthew Laird <psort-mail@sfu.ca> — Brinkman Lab, Simon Fraser University, Canada. shoutout to the whole lab, they understood the assignment 💜

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👑 SEE ALSO 👑

• Bio::Tools::Motif::Pattern
• Bio::Tools::Motif::Match

go read those too, iykyk 🫶

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💫 ACKNOWLEGEMENTS 💫

(yes bestie, that's how the original spells it — we don't touch the spelling, we just respect it 💅)

thanks go out to Fiona Brinkman, Jennifer Gardy and the other members of the Simon Fraser University Brinkman laboratory. literal legends, no notes 🌸

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💀 POD ERRORS 💀

not me having to report this 😭 but the doc had some coding errors, and here's what they were:

• Around line 99:
  • =pod directives shouldn't be over one line long! Ignoring all 2 lines of content

so yeah, two whole lines of content got ignored because of a =pod directive stretching past one line. we move on, we heal, we fix the pod next time 🩹

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that's the whole page bestie, every option, every arg, every last detail — nothing skipped, nothing invented. periodt. 🎀✨🦋

— written up for perl v5.34.0, dated 2022-02-06 💖 (that's the version and date from the original footer, in case you were wondering — mwah, bye!)