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

💖 Bio::T...n::Seg 💖

okay bestie, gather round, because we're talking about Bio::Tools::Run::Seg — a Perl module from the User Contributed Perl Documentation collection, and it's giving low complexity region detector energy. ✨

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🌸 NAME 🌸

Bio::Tools::Run::Seg — the object that hunts down low complexity regions in a given protein sequence. yes bestie, it's literally a little factory for spotting the repetitive, boring bits of your protein. 🦋

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✨ SYNOPSIS ✨

here's the vibe, copy-paste ready, not a single character changed:

# Build a Seg factory
# $paramfile is the full path to the seg binary file
my @params = ('PROGRAM',$paramfile);
my $factory = Bio::Tools::Run::Seg->new($param);

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

so you build the factory, you hand it a Bio::Seq object, and it hands you back an array of Bio::SeqFeature::Generic objects. periodt. 💅

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🧚 DESCRIPTION 🧚

Seg is a program that identifies low complexity regions in proteins. it was developed by Wootton and Federhen at NCBI. that's the whole lore, no cap. 👑

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🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

user feedback is an integral part of the evolution of this and other Bioperl modules. 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. many experienced and responsive experts will be able look at the problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible. the more deets you give, the faster the glow-up on your bug. 💖

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. bug reports can be submitted via the web:

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

bestie, do NOT suffer in silence. file the bug. the maintainers want to know. 🫶

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👑 AUTHOR - Bala 👑

Email savikalpa@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 a _ — so if you see an underscore, that's a "look but don't touch" situation, iykyk. 🙈

🍓 program_name 🍓

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

🍓 program_dir 🍓

• Title — program_dir
• Usage — $factory->program_dir(@params)
• Function — returns the program directory, obtained from ENV variable.
• Returns — string, or undef if $SEGDIR not in ENV
• Args — None

🍓 new 🍓

• Title — new
• Usage — $rm->new(@params)
• Function — creates a new Seg factory
• Returns — Bio::Tools::Run::Seg
• Args —

🍓 predict_protein_features 🍓

• Title — predict_protein_features()
• Usage — DEPRECATED Use $obj->run($seq) instead
• Function — Runs Seg and creates an array of features
• Returns — An array of Bio::SeqFeature::Generic objects
• Args — A Bio::PrimarySeqI

okay so this one is deprecated, which means it's the ex you don't text back. use run instead. 💀

🍓 run 🍓

• Title — run
• Usage — $obj->run($seq)
• Function — Runs Seg and creates an array of features
• Returns — An array of Bio::SeqFeature::Generic objects
• Args — A Bio::PrimarySeqI

🍓 _input 🍓

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

🍓 _run 🍓

• Title — _run
• Usage — $obj->_run()
• Function — Internal (not to be used directly)
• Returns — An array of Bio::SeqFeature::Generic objects
• Args — None

🍓 _writeSeqFile 🍓

• Title — _writeSeqFile
• Usage — obj->_writeSeqFile($seq)
• Function — Internal (not to be used directly)
• Returns — string - Fasta filename to which $seq was written
• Args — Bio::Seq object

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that's the whole page bestie, every single option and method accounted for, nothing skipped, we ate and left no crumbs. 🎀

and for the record, this whole thing is perl v5.36.0, dated 2023-01-22, so if you're reading this in the future, that's the era it came from. stay low complexity, stay iconic. 💜✨