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

💖 Bio::Tools::Run::Genemark 💖

okay bestie, welcome to the Bio::T...enemark(3pm) page — part of the User Contributed Perl Documentation, and literally your new fave wrapper for the GeneMark family of programs. let's get into it 🦋

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✨ NAME ✨

Bio::Tools::Run::Genemark — it's a Wrapper for local execution of the GeneMark family of programs. no cap, that's the whole vibe.

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✨ SYNOPSIS ✨

# GeneMark.hmm (prokaryotic)
my $factory =
    Bio::Tools::Run::Genemark->new('-program' => 'gmhmmp',
                                   '-m'       => 'model.icm');

# Pass the factory Bio::Seq objects
# returns a Bio::Tools::Genemark object
my $genemark = $factory->run($seq);

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✨ DESCRIPTION ✨

So basically this is a wrapper module for the GeneMark family of programs. it should work with all flavors of GeneMark.hmm at least — though bestie, ngl, only the prokaryotic version has actually been tested. so like... fingers crossed 🤞

General information about GeneMark lives at <http://exon.gatech.edu/GeneMark/>.

And if you need contact info for licensing inquiries, it's right here: <http://opal.biology.gatech.edu/GeneMark/contact.html>

⚠️ IMPORTANT, READ THIS ONE: GeneMark.hmm (prokaryotic at least) will only process the first sequence in a fasta file. so if you run() more than one sequence at a time, only the first one gets processed. the rest just sit there. periodt. 💀

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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. lots of experienced and responsive experts will be able to 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 the better, iykyk ✨

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of 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 - Mark Johnson 👑

Email: johnsonm-at-gmail-dot-com

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (you know, the little secret ones 🙈).

🔧 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   : $genemark->new(@params)
Function: creates a new Genemark factory
Returns:  Bio::Tools::Run::Genemark
Args    :

🔧 run

Title   :   run
Usage   :   $obj->run($seq_file)
Function:   Runs Genemark
Returns :   A Bio::Tools::Genemark 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::Genemark
Args    :   file name, sequence identifier (optional)

🔧 _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

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and that's the whole page, bestie!! you ate that 💅

this little masterpiece is brought to you by perl v5.36.0, dated 2023-01-22, and it's the Bio::T...enemark(3pm) page. go forth and wrap some GeneMark 🧚💜