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

💖 Bio::Tools::Run::tRNAscanSE 💖

okay bestie so this is the Bio::Tools::Run::tRNAscanSE page from the User Contributed Perl Documentation — it's the wrapper module that lets you run tRNAscan-SE from your own machine, straight from Perl. 🧬✨

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🌸 NAME 🌸

Bio::Tools::Run::tRNAscanSE — literally just a wrapper for running tRNAscan-SE locally. that's the whole job. 💅

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✨ SYNOPSIS ✨

here's the vibe, copy-paste girlies:

my $factory = Bio::Tools::Run::tRNAscanSE->new(-program => 'tRNAscan-SE');

# Pass the factory Bio::Seq objects,
# returns a Bio::Tools::tRNAscanSE object
my $factory = $factory->run($seq);
or
my $factory = $factory->run(@seq);

so you hand the factory some Bio::Seq objects, and it hands you back a Bio::Tools::tRNAscanSE object. one seq or a whole squad of them, your call. 🫶

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🦋 DESCRIPTION 🦋

it's a wrapper module for tRNAscan-SE. that's it, that's the description. 💜

tRNAscan-SE is open source and you can grab it at <http://lowelab.ucsc.edu/software/>. no cap, go get it. 🌈

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is like, an integral part of the evolution of this and every other Bioperl module. so send your comments and suggestions to one of the Bioperl mailing lists, preferably. your participation is much appreciated — we're obsessed with you for it. 🎀

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

🫂 Support

usage questions? support issues? direct them to the mailing list:

bioperl-l@bioperl.org

not to the module maintainer directly, bestie. please. 😭

the reason is that there are so many experienced and responsive experts on the list who can look at your problem and address it quickly. if at all possible, include a thorough description of the problem with code and data examples — receipts, basically. 📝

🐛 Reporting Bugs

found a bug? report it to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions. bug reports can be submitted via the web at:

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

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👑 AUTHOR - Mark Johnson 👑

Email: johnsonm-at-gmail-dot-com

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📖 APPENDIX 📖

the rest of the docs detail each of the object methods, one by one. internal methods usually get an underscore _ in front of them — that's your sign they're backstage, not main character. 🌟

program_name

• Title: program_name
• Usage: $factory>program_name()
• Function: gets/sets the program name
• Returns: string
• Args: string

program_dir

• Title: program_dir
• Usage: $factory->program_dir()
• Function: gets/sets the program dir
• Returns: string
• Args: string

new

• Title: new
• Usage: $tRNAscanSE->new(@params)
• Function: creates a new tRNAscanSE factory
• Returns: Bio::Tools::Run::tRNAscanSE
• Args: (none listed)

run

• Title: run
• Usage: $obj->run($seq_file)
• Function: Runs tRNAscan-SE
• Returns: A Bio::Tools::tRNAscanSE object
• Args: An array of Bio::PrimarySeqI objects

_run

• Title: _run
• Usage: $obj->_run()
• Function: Internal (not to be used directly)
• Returns: An instance of Bio::Tools::tRNAscanSE
• Args: file name

⚠️ internal!! do not use directly, i am begging. 🙈

_write_seq_file

• Title: _write_seq_file
• Usage: obj->_write_seq_file($seq) or obj->_write_seq_file(@seq)
• Function: Internal (not to be used directly)
• Returns: Name of a temp file containing program output
• Args: One or more Bio::PrimarySeqI objects

⚠️ also internal, also not for direct use. the underscore is a boundary, respect it. 💀

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and that's the whole page, bestie!! this one's from perl v5.36.0, dated 2023-01-22, and it's part of the User Contributed Perl Documentation for Bio::T...AscanSE(3pm) — slay, ate, no notes. 💖✨🎀🦋🌸💅🫶