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

📦
version 1.7.3 · 3 versions
, in debian bookworm, ubuntu noble

✨ NAME ✨

Bio::Tools::Run::Glimmer — bestie, it's a wrapper for running Glimmer, GlimmerM and GlimmerHMM locally on your own machine 💅

(oh and btw, this lives in the User Contributed Perl Documentation corner of the man universe, just so u know where u are 🫶)

🌸 SYNOPSIS 🌸

okay so here's the whole vibe, copy-paste ready, no notes:

# glimmer2
my $factory =
    Bio::Tools::Run::Glimmer->new('-program' => 'glimmer3',
                                  '-model'   => 'model.icm');
# glimmer3
my $factory =
    Bio::Tools::Run::Glimmer->new('-program' => 'glimmer2',
                                  '-model'   => 'model.icm');
# glimmerm
my $factory =
    Bio::Tools::Run::Glimmer->new('-program' => 'glimmerm');

# glimmerHMM
my $factory =
    Bio::Tools::Run::Glimmer->new('-program' => 'glimmerHMM');

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

(and yes bestie, those comments are literally what the original says, we do NOT edit the source material around here, we respect the text 😌)

💖 DESCRIPTION 💖

It's a wrapper module for the whole Glimmer family of programs 🧚 It's supposed to work with every flavor that's currently out there — Glimmer, GlimmerM and GlimmerHMM. But real talk? Only Glimmer 2.X and 3.X have actually been tested. The rest is giving "trust me bro" energy, no cap.

⚠️ heads up bestie: Glimmer 2.X 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 others are just standing there like 🧍 not invited to the party. periodt.
🚨 another one: Glimmer 3.X produces two output files. This module only passes the .predict file over to Bio::Tools::Glimmer. The other file is on its own, living its truth, unbothered 💀

📬 FEEDBACK 📬

🌈 Mailing Lists 🌈

User feedback is, like, an integral part of the evolution of this module and all the other Bioperl modules 🦋 Send ur comments and suggestions preferably to one of the Bioperl mailing lists — your participation is so so appreciated, fr fr:

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

🫶 Support 🫶

okay listen: please send usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

...rather than sliding into the module maintainer's DMs directly 🙈 There are so many experienced and responsive experts on that list who can look at ur problem and fix it fast. And please, when you write in, include a thorough description of the problem with code and data examples if it's at all possible — it's giving helpful, it's giving iconic 👑

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions together, as a team 💜 Bug reports can be submitted via the web:

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

👑 AUTHOR — Mark Johnson 👑

Email: johnsonm-at-gmail-dot-com

🎀 APPENDIX 🎀

The rest of this documentation details each of the object methods, one by one, no skips. Internal methods are usually preceded with a _ (that underscore is basically their "staff only" lanyard, iykyk).

program_name

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

Gets or sets the program name — give it a string, get a string back 💅

program_dir

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

Gets or sets the program directory. String in, string out, we love a simple relationship ✨

model

Title   : model
Usage   : $factory>model()
Function: gets/sets the name of the model (icm) file
Returns:  string
Args    : string

Gets or sets the name of the model (icm) file 🌸 string in, string out, no drama.

new

Title   : new
Usage   : $glimmer->new(@params)
Function: creates a new Glimmer factory
Returns:  Bio::Tools::Run::Glimmer
Args    :

Creates a brand new Glimmer factory 🏭 main character constructor energy.

run

Title   :   run
Usage   :   $obj->run($seq_file)
Function:   Runs Glimmer/GlimmerM/GlimmerHMM
Returns :   A Bio::Tools::Glimmer object
Args    :   An array of Bio::PrimarySeqI objects

Runs Glimmer/GlimmerM/GlimmerHMM, hands you back a Bio::Tools::Glimmer object, and it wants an array of Bio::PrimarySeqI objects to chew on 🔥

_run

Title   :   _run
Usage   :   $obj->_run()
Function:   Internal(not to be used directly)
Returns :   An instance of Bio::Tools::Glimmer
Args    :   file name, sequence identifier (optional)
Internal — do NOT use this directly bestie. It takes a file name and an optional sequence identifier, and returns an instance of Bio::Tools::Glimmer. Stay in ur lane, let the module handle it 🙈

_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 🙅 Feed it one or more Bio::PrimarySeqI objects and it returns the name of a temp file containing the program output. Lowkey the backbone of the whole operation tbh.

and that's the whole page, we ate and left no crumbs 🍓 thanks for reading bestie, go annotate some genomes 💖

signing off — this was perl v5.36.0, dated 2023-01-22, straight from the Bio::T...limmer(3pm) page. mwah 💋

📦 where this page comes from