Bio::S...meSubs(3pm)

💖 Bio::SeqIO::game::gameSubs — a base class for game-XML parsing 💖

okay bestie, so this is Bio::SeqIO::game::gameSubs(3pm), straight out of the User Contributed Perl Documentation, and we are gonna get you so comfy with it. it's a little base-class baddie that handles game-XML parsing. no cap.

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✨ SYNOPSIS ✨

Not used directly

yeah. she's not a "call me up and use me" kind of module. she's a base class. she's the backstage crew. iconic, but not for direct use. 💅

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🌸 DESCRIPTION 🌸

literally a whole bag of tricks for game-XML parsing. ✨

the PerlSAX handler methods were stolen from Chris Mungall's XML base class, which he in turn stole from Ken MacLeod's XML::Handler::Subs. so this is like... ancestral theft. generational. we love to see it. 💀

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🫶 FEEDBACK 🫶

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. send your comments and suggestions — preferably to one of the Bioperl mailing lists.

your participation is much appreciated. genuinely. 🥹

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. why? because many experienced and reponsive experts will be able look at the problem and quickly address it. bestie, the group chat is faster than the DM. periodt. 💅

please include a thorough description of the problem with code and data examples if at all possible. help them help you. 🎀

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

go off, file that issue. 🔥

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👑 AUTHOR - Sheldon McKay

Email mckays@cshl.edu

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — that's the secret handshake, iykyk. 🤫

🆕 new

• Title : new
• Usage : not used directly
• Returns : a gameHandler object
• Args : an XML filename

🏃 go

• Title : go
• Usage : not used directly
• Function : starts PerlSAX XML parsing

🎬 start_document

• Title : start_document
• Usage : not used directly

🎞️ end_document

• Title : end_document
• Usage : not used directly

🧩 start_element

• Title : start_element
• Usage : not used directly

🧷 end_element

• Title : end_element
• Usage : not used directly

🔤 characters

• Title : characters
• Usage : not used directly

🧼 strip_characters

• Title : strip_characters
• Usage : not used directly
• Function : cleans up XML element contents

🎯 curr_element

• Title : curr_element
• Usage : not used directly
• Function : returns the currently open element

🌿 flush

• Title : flush
• Usage : $self->flush($element) # or $element->flush
• Function : prune a branch from the XML tree
• Returns : true if successful
• Args : an element object (optional)

not me pruning branches like a lil gardener 🧚 — optional arg, true on success, that's the whole deal.

😤 complain

• Title : complain
• Usage : $self->complain("This is terrible; I am not happy")
• Function : throw a non-fatal warning, formats message for pretty-printing
• Returns : nothing
• Args : a list of strings

🔗 dbxref

• Title : dbxref
• Usage : $self->db_xref($el, $tags)
• Function : an internal method to flatten dbxref elements
• Returns : the db_xref (eg wormbase:C02D5.1)
• Args : an element object (reqd) and a hash ref of tag/values (optional)

💬 comment

• Title : comment
• Usage : $self->comment($comment_element)
• Function : a method to flatten comment elements
• Returns : a string
• Args : an comment element (reqd) and a hash ref of tag/values (optional)
• Note : The hope here is that we can unflatten structured comments in game-derived annotations happen to make a return trip

lowkey manifesting that round trip for these structured comments 🦋

🏷️ property

• Title : property
• Usage : $self->property($property_element)
• Function : an internal method to flatten property elements
• Returns : a hash reference
• Args : an property/output element (reqd) and a hash ref of tag/values (optional)
• Note : This method is aliased to 'output' to handle structurally identical output elements

🔍 evidence

• Title : evidence
• Usage : $self->evidence($evidence_element)
• Function : a method to flatten evidence elements
• Returns : a string
• Args : an evidence element

📅 date

• Title : date
• Usage : $self->date($date_element)
• Function : a method to flatten date elements
• Returns : true if successful
• Args : a date element

🧬 protein_id

• Title : protein_id
• Usage : $pid = $self->protein_id($cds, $standard_name)
• Function : a method to search for a protein name
• Returns : a string
• Args : the CDS object plus the transcript's 'standard_name'

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okay that's the whole page, bestie, you ate it. 💖✨

this little masterpiece shipped with perl v5.32.1, dated 2021-08-15, and yes it's still Bio::S...meSubs(3pm) in the corner like a cute lil watermark. bye, go parse some game-XML. 🎀🦋🌈