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

💖 Bio::Tools::Run::Genscan 💖

okay bestie, welcome to the User Contributed Perl Documentation glow-up of Bio::T...enscan(3pm) — she's a whole icon and she's about to tell you how to find genes. no cap. 🧬✨

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✨ NAME ✨

Bio::Tools::Run::Genscan — it's an object that identifies genes in a given sequence, given a matrix (for the appropriate organisms, obviously 💅).

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🌸 SYNOPSIS 🌸

bestie, this is the whole vibe in four lines:

# Build a Genscan factory
my $param = ('MATRIX'=>HumanIso.smat);
my  $factory = Bio::Tools::Run::Genscan->new($param);

# Pass the factory a Bio::Seq object
#@genes is an array of Bio::Tools::Predictions::Gene objects
my @genes = $factory->run($seq);

like, build the factory, hand her a Bio::Seq object, and @genes comes back as an array of Bio::Tools::Predictions::Gene objects. we love a clean pipeline. 🫶

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🦋 DESCRIPTION 🦋

Genscan is a gene-identifying program, and she was developed by Christopher Burge at http://genes.mit.edu/burgelab/ — give credit where credit is due, periodt. 👑

By default, she goes looking for an executable called genscan plus the data/parameter files in the directory that the GENSCANDIR environmental variable points at. that's the default, that's the whole thing. no guessing required. ⭐

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is literally an integral part of the evolution of this and other Bioperl modules — so like, your comments and suggestions? send them, 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

okay so for usage questions or support issues, please direct them to the mailing list:

bioperl-l@bioperl.org

…rather than going straight to the module maintainer. there are so many experienced and responsive experts who can look at your problem and quickly address it, fr fr. and if at all possible, please include a thorough description of the problem with code and data examples. receipts help everyone. 🙈

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — it's giving teamwork, it's giving accountability. Bug reports can be submitted via the web at:

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

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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 that underscore, bestie, that's a do not touch energy. 🙅‍♀️

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🔧 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    :

🧬 predict_genes()

Title   :   predict_genes()
Usage   :   DEPRECATED: use $obj->run($seq) instead
Function:   Runs genscan and creates an array of Genes
Returns :   An array of Bio::Tools::Prediction::Gene objects
Args    :   A Bio::PrimarySeqI

ok so this one is DEPRECATED — use $obj->run($seq) instead. she's retired, she's living her best life, let her rest. 💀

🏃 run

Title   :   run
Usage   :   $obj->run($seq)
Function:   Runs genscan and creates an array of Genes
Returns :   An array of Bio::Tools::Prediction::Gene objects
Args    :   A Bio::PrimarySeqI

🙈 _run

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

internal, bestie. not to be used directly. we said what we said. 💅

🙈 _set_input()

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

also internal. also not to be used directly. keep scrolling. 🎀

🙈 _writeSeqFile()

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

yep, internal again, not to be used directly. that's the trio. ✨

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and that's the whole page, bestie — slay, go find some genes 💖🧬✨

this was Bio::T...enscan(3pm) brought to you by perl v5.36.0, dated 2023-01-22. mwah. 🫶🎀