Bio::T...n::Coil(3pm)

💖 Bio::T...n::Coil(3pm) — the vibe-y guide 💖

okay bestie, so this is a page from the User Contributed Perl Documentation, and it's literally called Bio::T...n::Coil — the Perl module that wraps the whole ncoils situation. it's giving "perl module documentation" but make it make sense. let's go 🦋

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✨ NAME ✨

Bio::Tools::Run::Coil — it's a wrapper for the ncoils program. that's the whole name. short, sweet, iconic. 💅

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🌸 SYNOPSIS 🌸

here's the group chat version of how you'd actually use it:

# Build a Coil factory
my $factory = Bio::Tools::Run::Coil->new($params);

# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq);

so like — you build a factory, then you hand it a seq, and it hands you back features. no cap, that's it. 🎀

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🧚 DESCRIPTION 🧚

okay so this module? it's a wrapper for the ncoils program, which you can grab over at http://www.russell.embl-heidelberg.de/coils/coils.tar.gz. what does ncoils do, you ask? it predicts coiled coils in protein sequences. protein gossip, basically. 💀

by default, it goes looking for an executable called ncoils plus the data/parameter files in the directory that the COILSDIR environmental variable points at. so yeah, set that env var or it's gonna be searching like it lost its airpods. 🫶

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📚 REFERENCES 📚

the receipts, bestie, in order:

• Lupas, van Dyke & Stock, Predicting coiled coils from protein sequences, Science 252:1162-1164, 1991.
• Lupas, A., Prediction and Analysis of Coiled-Coil Structures, Meth. Enzymology 266:513-525, 1996.

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

user feedback is literally an integral part of the evolution of this and other Bioperl modules — like, the whole thing grows because people talk. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, fr fr. 🥹

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫂 Support 🫂

please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

…rather than to the module maintainer directly. why? because so many experienced and responsive experts will be able to look at the problem and quickly address it — it's a whole squad, not one person. 💪

also, if at all possible, please include a thorough description of the problem with code and data examples. thorough. like, give them the whole lore. 📖

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system — that's how we keep track of the bugs and their resolutions, together, as a community. bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

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👑 AUTHORS 👑

• Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil, originally written by Marc Sohrmann (ms2@sanger.ac.uk)
• Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>

# Please direct questions and support issues to <bioperl-l@bioperl.org>
#

• Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org) 🐡

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🔍 APPENDIX 🔍

the rest of the documentation details each of the object methods. internal methods are usually preceded with an underscore — _ — so if you see one, that's your sign it's an inside-job method, iykyk. 🙈

⭐ program_name ⭐

Title   : program_name
Usage   : $factory>program_name()
Function: holds the program name
Returns:  string
Args    : None

it holds the program name. that's the job. returns a string, takes no args. simple queen behavior. ✨

⭐ program_dir ⭐

Title   : program_dir
Usage   : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns:  string
Args    :

returns the program directory, and it gets that straight from the ENV variable. returns a string, no args listed. 🌈

⭐ new ⭐

Title   : new
Usage   : $coil->new(@params)
Function: creates a new Coil factory
Returns:  Bio::Tools::Run::Coil
Args    :

creates a new Coil factory — main character constructor energy right here. returns a Bio::Tools::Run::Coil. no args listed. 👑

⭐ predict_protein_features ⭐

Title   :   predict_protein_features()
Usage   :   DEPRECATED. Use $obj->run instead.
Function:   Runs Coil and creates an array of featrues
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :   A Bio::PrimarySeqI

🚨 DEPRECATED. like, do not use this one, bestie — use $obj->run instead. it runs Coil and creates an array of features (spelled featrues in the original, and we respect the original 💀), returns an array of Bio::SeqFeature::Generic objects, and takes a Bio::PrimarySeqI as its arg.

⭐ run ⭐

Title   :   run
Usage   :   $obj->run($seq)
Function:   Runs Coil and creates an array of featrues
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :   A Bio::PrimarySeqI, or a Fasta filename.

this is the one you actually want. it runs Coil and creates an array of features, returns an array of Bio::SeqFeature::Generic objects, and its arg is a Bio::PrimarySeqI, or a Fasta filename. either one, you're covered. 🔥

⭐ _input ⭐

Title   :   _input
Usage   :   obj->_input($seqFile)
Function:   Internal(not to be used directly)
Returns :
Args    :

internal — not to be used directly, so hands off, bestie. 🙅

⭐ _run ⭐

Title   :   _run
Usage   :   $obj->_run()
Function:   Internal(not to be used directly)
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :

also internal — not to be used directly. returns an array of Bio::SeqFeature::Generic objects. no args listed. 💅

⭐ _writeSeqFile ⭐

Title   :   _writeSeqFile
Usage   :   obj->_writeSeqFile($seq)
Function:   Internal(not to be used directly)
Returns :
Args    :

internal — not to be used directly. returns nothing, args blank. the mystery method. 🕵️♀️

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and that's the whole page, bestie!! 🎀 this one came from perl v5.36.0 dated 2023-01-22, under the manual name Bio::T...n::Coil(3pm). go forth and predict some coiled coils, you absolute icon. slay. 💖🦋✨