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

💖 Bio::T...ponine — the Bio::Tools::Run::Eponine era 💖

okay bestie, sit down, hydrate, because we're about to talk about Bio::Tools::Run::Eponine — the Perl wrapper that runs Eponine, aka your fave mammalian TSS predictor 🧬✨. This page lives in the User Contributed Perl Documentation section of the manual, and honestly? it ate.

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✨ NAME ✨

Bio::Tools::Run::Eponine — an object for execution of the Eponine, which is a mammalian TSS predictor. periodt. 💅

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🌸 SYNOPSIS 🌸

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

use Bio::Tools::Run::Eponine;
use strict;
my $seq = "/data/seq.fa";
my $threshold  = "0.999";
my @params = ( '-seq' => $seq,
               '-threshold' => $threshold,
               '-epojar'  => '/usr/local/bin/eponine-scan.jar',
                '-java'  => '/usr/local/bin/java');

my $factory = Bio::Tools::Run::Eponine->new(@params);
# run eponine against fasta
my $r = $factory->run($seq);
my $parser = Bio::Tools::Eponine->new($r);

while (my $feat = $parser->next_prediction){
        #$feat contains array of SeqFeature
        foreach my $orf($feat){
                print $orf->seqname. "\n";
        }
}

# Various additional options and input formats are available.  See
# the DESCRIPTION section for details.

like, build the factory, run it against the fasta, hand the result to the parser, loop through the predictions, print the seqname. iconic. 🦋

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🎀 DESCRIPTION 🎀

it's a wrapper for eponine, a mammalian TSS predictor. that's the whole gig bestie, and it does it well. 🫶

now the IMPORTANT part, do not scroll past this:

The environment variable EPONINEDIR must be set to point at either the directory which contains eponine-scan.jar or directly at the jar which eponine-scan classfiles. NOTE: EPONINEDIR must point at the real file, not a symlink. 🚨

like fr fr, the real file. the symlink will not save you. 😭

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💌 FEEDBACK 💌

Mailing Lists 📬

user feedback is an integral part of the evolution of this and other Bioperl modules — literally, it's the glow-up juice. 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. 👑

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 👑

email gisoht@nus.edu.sg 📧

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🧚 APPENDIX 🧚

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, that underscore means don't touch unless you know). 🙈

java ☕

• Title: java
• Usage: $obj->java('/usr/opt/java130/bin/java');
• Function: Get/set method for the location of java VM
• Args: File path (optional)

epojar 🫙

• Title: epojar
• Usage: $obj->epojar('/some/path/to/eponine-scan.jar');
• Function: Get/set method for the location of the eponine-scan executable JAR
• Args: Path (optional)

threshold 🎚️

• Title: threshold
• Usage: my $threshold = $self->threshold
• Function: Get/Set the threshold for Eponine
• Returns: string
• Args: b/w 0.9 and 1.0

run 🏃♀️

• Title: run
• Usage: my @genes = $self->run($seq)
• Function: runs Eponine and creates an array of features
• Returns: An Array of SeqFeatures
• Args: A Bio::PrimarySeqI

predict_TSS 🔮

• Title: predict_TSS
• Usage: Alias for run()

_setinput() 📝

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: writes input sequence to file and return the file name
• Example:
• Returns: string
• Args:

not to be called directly, bestie. that's the whole point of the underscore. 💀

_run_eponine ⚙️

• Title: run_eponine
• Usage: $obj->_run_eponine()
• Function: execs the Java VM to run eponine
• Returns: none
• Args: none

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and that's the whole page, no cap. this was perl v5.36.0, dated 2023-01-22, from the User Contributed Perl Documentation corner of the manual. stay slaying, stay thresholding between 0.9 and 1.0, and go predict some TSS. 💅✨🎀🦋