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

🎀 NAME 🎀

ok so welcome to the GO::Pa...parser(3pm) page, which lives in the User Contributed Perl Documentation corner of the internet 🫶

GO::Parsers::base_parser — the base class for parsers. she's the blueprint. the blueprint-iest blueprint. the mother of all parsers 💅

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✨ SYNOPSIS ✨

do not use this class directly; use GO::Parser

real talk bestie: do NOT come for this class directly 🙅‍♀️ she is a base class, she is not the moment. go use GO::Parser instead. periodt.

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💜 DESCRIPTION 💜

so the DESCRIPTION section… is empty. like, genuinely blank. she said "no thoughts, head empty" 🫥✨

ngl that's fine, because everything you actually need is down in the methods below, so scroll, bestie, we got you 🦋

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👑 AUTHOR 👑

also blank 🙈 zero content, no name, no credit, no nothing. anonymous era, we respect it. we move.

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💅 show_messages

• Usage — not documented. mysterious ✨
• Returns — nothing listed 🫥
• Args — nothing listed either

three for three on the blanks, she's giving minimalism, iykyk 💀

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🧚 normalize_files

• Usage — @files = $parser->normalize_files(@files)
• Returns — nothing listed in the original 🌸
• Args — also nothing listed

ok so what she actually does: you hand her a list of filenames/paths, and she "glob"s them, then uncompresses any compressed files, and hands you back the new file list 🎀

so basically: messy file list goes in, tidy file list comes out. slay.

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🦋 litemode

• Usage — $p->litemode(1)
• Returns — nothing listed 🫥
• Args — bool

when you set this, the parser only throws the following events:

id|name|is_a|relationship|namespace

(optimisation for fast parsing) 🏎️✨ so yes, she's the "i don't need the whole story, just the highlights" mode. litemode arc.

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🌸 acc2name_h

• Usage — $n = $p->acc2name_h->{'GO:0003673'}
• Returns — hashref
• Args — hashref [optional]

gets/sets a hash mapping IDs to names 💖

this will be automatically set by an ontology parser.

a non-ontology parser will use this index to verify the parsed data — see $p->acc_not_found($id), below. spooky foreshadowing, but make it data validation 🔍

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👑 acc_not_found

• Usage — if ($p->acc_not_found($go_id)) { warn("$go_id not known") }
• Returns — bool
• Args — acc string

uses acc2name_h — if this hash mapping has been created AND the acc is not in the hash, THEN it is considered not found. yes bestie the all-caps is doing a lot but she means it.

this is useful for non-ontology parsers (xref_parser, go_assoc_parser) to check whether a referenced ID is actually present in the ontology 🌈

⚠️ MAJOR NOTE, DO NOT SKIP THIS ONE: if acc2name_h has not been created, then accs cannot be considered not-found, and this will always return 0/false. like, always. she will look you dead in the eye and say everything's fine even when it isn't 💀 so make sure that hash exists before you trust a false, fr fr.

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and that's the whole page, no cap 🫶 this one was perl v5.36.0, dated 2023-12-18, and it's the GO::Pa...parser(3pm) manual entry — mwah, go parse something iconic 💋👑