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

💖 Bio::Tools::Run::Signalp — the perl manpage, but make it cute 💖

okay bestie, so this is Bio::T...ignalp(3pm), a User Contributed Perl Documentation page, and it's literally the wrapper for the Signalp program. she's giving "small module, big feelings" energy and i'm obsessed 💅

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✨ NAME ✨

Bio::Tools::Run::Signalp — a wrapper for the Signalp program 🧬✨

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🌸 SYNOPSIS 🌸

Build a Signalp factory, babe:

Build a Signalp factory

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

so real: you make the factory, you hand it a Bio::Seq, and @feats comes back as an array of Bio::SeqFeature::Generic objects. iconic behaviour fr fr 🫶

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🦋 DESCRIPTION 🦋

it's a wrapper module for the Signalp program. that's the whole vibe. no cap. 🎀

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, the whole glow-up depends on it. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated 💖

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 reponsive 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. slay responsibly ✨

🐛 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/

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👑 AUTHOR 👑

• based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp
• originally written by Marc Sohrmann (ms2@sanger.ac.uk)
• written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
• contributions by David Vilanova (david.vilanova@urbanet.ch), Shawn Hoon (shawnh@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) — main character energy, honestly 💜

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _. 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
• Args :

🌟 new

• Title : new
• Usage : my $factory= Bio::Tools::Run::Signalp->new();
• Function: creates a new Signalp factory
• Returns: Bio::Tools::Run::Signalp
• Args :

🚨 predict_protein_features

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

bestie, do not use this one, it's deprecated 😭 use $factory->run($seq) like the cool kids.

🏃 run

• Title : run()
• Usage : my $feats = $factory->run($seq)
• Function: Runs Signalp
• Returns : An array of Bio::SeqFeature::Generic objects
• Args : A Bio::PrimarySeqI

📥 _input

• Title : _input
• Usage : $factory->_input($seqFile)
• Function: get/set for input file
• Returns :
• Args :

⚙️ _run

• Title : _run
• Usage : $factory->_run()
• Function: Makes a system call and runs signalp
• Returns : An array of Bio::SeqFeature::Generic objects
• Args :

✍️ _writeSeqFile

• Title : _writeSeqFile
• Usage : $factory->_writeSeqFile($seq)
• Function: Creates a file from the given seq object
• Returns : A string(filename)
• Args : Bio::PrimarySeqI

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and that's the whole page, bestie 💅 this was perl v5.36.0, dated 2023-01-22, and it's the Bio::T...ignalp(3pm) manpage — ate and left no crumbs 🍓✨ bye bye! 💖🦋🌸