GO::Pa...parser(3pm)

💖 NAME 💖

GO::Parsers::go_assoc_parser — the girl who does syntax parsing of GO gene-association flat files 🧚

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✨ SYNOPSIS ✨

(bestie the synopsis is literally empty, there's nothing here, the vibes are simply immaculate and unbothered 💅)

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💅 DESCRIPTION 💅

do not use this class directly; use GO::Parser 🚨 like, I am begging you, don't come for me directly, go through the front door.

Okay so what she actually does: this generates Stag/XML event streams from GO association files. 🌸 Examples of these files can be found at http://www.geneontology.org, and here's what an example of lines from an association file looks like, look at her go:

SGD     S0004660        AAC1            GO:0005743      SGD:12031|PMID:2167309 TAS             C       ADP/ATP translocator    YMR056C gene    taxon:4932 20010118
SGD     S0004660        AAC1            GO:0006854      SGD:12031|PMID:2167309 IDA             P       ADP/ATP translocator    YMR056C gene    taxon:4932 20010118

See http://www.geneontology.org/GO.annotation.shtml#file 🦋

Also see http://www.godatabase.org/dev/xml/dtd/go_assoc-parser-events.dtd — that's for the DTD of the event stream that is generated, iykyk.

The following stag-schema describes the events that are generated in parsing an assoc file, and honestly? it's giving family tree, it's giving ancestry dot com 🎀:

(assocs
 (dbset+
   (proddb "s")
   (prod+
     (prodacc "s")
     (prodsymbol "s")
     (prodtype "s")
     (prodtaxa "i")
     (assoc+
       (assocdate "i")
       (source_db "s")
       (termacc "s")
       (is_not "i")
       (aspect "s")
       (evidence+
         (evcode "s")
         (ref "s"))))))

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and that's the whole page bestie, short and iconic, no notes 👑✨

this was perl v5.36.0, dated 2023-12-18, part of the GO::Pa...parser(3pm) story, filed under User Contributed Perl Documentation — mwah, love u, go parse something gorgeous 💖🦋