GO::Mo...iation(3pm)

💖 NAME 💖

GO::Model::Association — bestie, it's an association between a GO term and a gene product. That's the whole vibe. GO::Model::Association(3pm) is the manual page name, for the record, and it lives in the User Contributed Perl Documentation corner of the world. 🫶

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✨ SYNOPSIS ✨

Okay so here's the little starter pack. This is literally copy-paste energy, keep it exact:

# print all gene products associated with a GO::Model::Term
my $assoc_l = $term->association_list;
foreach my $assoc (@$assoc_l) {
  printf "gene product:%s %s %s (evidence: %s)\n",
    $assoc->gene_product->symbol,
    $assoc->is_not ? "IS NOT" : "IS",
    $term->name,
    map {$_->code} @{$assoc->evidence_list};
}

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🦋 DESCRIPTION 🦋

It represents an association between a GO term (GO::Model::Term) and a gene product (GO::Model::GeneProduct). Iconic little connector object, honestly. 💅

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go_public_acc

• Usage — -
• Returns — -
• Args — -

Yep, that's the whole thing. No notes. 🙈

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add_evidence

• Usage — - $assoc->add_evidence($my_evid);
• Returns — -
• Args — - GO::Model::Evidence

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evidence_list

• Usage — my $ev_l = $assoc->evidence_list;
• Returns — -
• Args — -

gets/sets arrayref of GO::Model::Evidence ✨

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evidence_as_str

• Usage — print $assoc->evidence_as_str
• Usage — print $assoc->evidence_as_str(1); #verbose
• Returns — -
• Args — - verbose

concatenates evcodes together, for display 🎀

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has_evcode

• Usage — if $assoc->has_evcode("IEA");
• Returns — - boolean
• Args — - evcode [string]

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remove_evcode

• Usage — $assoc->remove_evcode("IEA");
• Returns — -
• Args — - evcode [string]

removes all evidence of the specified type from the association; useful for filtering. so real. 🧚

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evidence_score

• Usage — my $score = $assoc->evidence_score
• Returns — - 0 <= float <= 1
• Args — -

returns a score for the association based on the evidence;

okay bestie, important: This is an EXPERIMENTAL method; it may be removed in future versions. So don't build your whole personality on it, lowkey. 😭

The evidence fields can be thought of in a loose hierarchy:

TAS
   IDA
      IMP/IGI/IPI
                 ISS
                    NAS

see http://www.geneontology.org/GO.evidence.html — go read, iykyk. 🔥

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gene_product

• Usage — my $gp = $assoc->gene_product
• Returns — -
• Args — -

gets sets GO::Model::GeneProduct 🌸

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assigned_by

• Usage — -
• Returns — -
• Args — -

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is_not

• Usage — -
• Returns — -
• Args — -

gets/sets boolean representing whether this relationship is negated. literally the IS NOT toggle, slay. 💅

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assocdate

• Usage — -
• Returns — -
• Args — -

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assocdate

• Usage — -
• Returns — -
• Args — -

gets/sets integer representing the date of the association (YYYYMMDD format) 📅

yes bestie it's listed twice in the original, and we are keeping every single detail, no cap. 👯‍♀️

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role_group

• Usage — -
• Returns — -
• Args — -

gets/sets integer to indicate which associations go together 👑

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and that's the whole page, periodt. this came from the perl v5.36.0 docs, dated 2023-12-18, and the footer calls it GO::Mo...iation(3pm) because apparently even manpage footers get the choppy abbreviation treatment. 💖✨🫶