SWISS::DRs(3pm)

💖 SWISS::DRs 💖

okay bestie, welcome to SWISS::DRs — this is the lil class that handles the DR (database crossreference) lines inside an SWISS-PROT + TrEMBL entry, exactly as specified in the user manual at http://www.expasy.org/sprot/userman.html. no cap, it's giving "I know everyone's cross-references and I'm not shy about it." ✨

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🌸 Inherits from 🌸

SWISS::ListBase.pm — yeah she's got a whole family tree, she's not doing this alone 🫶

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🎀 Attributes 🎀

• "list" — an array of arrays. each element is an array like (Database_identifier, primary_key, secondary_key[, further elements]). so basically a list of lists, each one a lil DR line's worth of facts. iconic behavior fr fr 💅

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🦋 Methods 🦋

⭐ Standard methods ⭐

• new
• fromText
• toText
• sort

these are the classics, the main character squad, the ones you already know and love 😌

🌈 Reading methods 🌈

• emblacs — returns a list of all EMBL accession numbers. these are the primary keys of EMBL crossreferences. like, every single one, bestie 💜
• pids [$dropVersion] — returns a list of all PIDs. these are the secondary keys of EMBL crossreferences.

⚠️ ATTENTION: the EMBL protein identifiers introduced in 1999 are of the form xxxxx.yy, e.g. CAA33128.1. if $dropVersion is set, the version number (.yy) will be dropped from each PID. so like… the .1 just ✨leaves✨.

Example — if the EMBL DR line is

DR   EMBL; L37685; AAC41668.1; -.

then pids(1) will only return AAC41668, NOT AAC41668.1. not me being dramatic about a version suffix but that's literally the whole point 😭

💀 Filter functions 💀

• dbName($dbTargetName) — true if the first element of a DR line (the DB name) matches $dbTargetName. and bestie, $dbTargetName has to match in full, not only a partial match. no vibes-based fuzzy matching here, it's all or nothing 🙈
• notDbName($dbTargetName) — true if the first element of a DR line (the DB name) does NOT match $dbTargetName. the hater version of the function above, lowkey useful tho 💅

🧚 ** lines (SWISS-PROT internal format) 🧚

each DR line may be followed by a ** line like

 **   DR   PROSITE; PS12345; XXX_PAT; FALSE_POS_1

these will be stored internally as DR lines with the DB identifier '_HIDDEN_'. so sneaky, so undercover, so slay 👑

therefore adding a ** PROSITE line is done as:

$entry->DRs->add(['_HIDDEN_', 'PS12345', 'XXX_PAT', 'FALSE_POS_1']);

see? you just pop the '_HIDDEN_' in as the DB identifier and she goes straight into the list like she was always there. periodt. 💖

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and that's the whole page, bestie!! this one shipped as part of perl v5.32.1, dated 2021-08-15, and it's filed under SWISS::DRs(3pm) in the User Contributed Perl Documentation. go forth and crossreference responsibly 🎀✨🌸🦋💜