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

💖 Bio::SeqIO::game::seqHandler — the game-XML sequence wrangler 💖

okay bestie, welcome to Bio::SeqIO::game::seqHandler, a lil class from the User Contributed Perl Documentation corner of the perl man pages. it handles game-XML sequences. that's the whole vibe. 🦋

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✨ NAME ✨

Bio::SeqIO::game::seqHandler — a class for handling game-XML sequences 🎀

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🌸 SYNOPSIS 🌸

This modules is not used directly

no cap, you don't call this one yourself. it's a backstage queen, not the main character. 💅

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💜 DESCRIPTION 💜

Bio::SeqIO::game::seqHandler processes all of the sequences associated with a game record and, via feature handlers, processes the associated annotations. it's giving middle-management for XML sequences and honestly? iconic. 👑

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🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

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

your participation is much appreciated. fr fr, they mean it. 🥹

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. many experienced and reponsive experts will be able look at the problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible. (yes, they spelled it "reponsive" — we keep it exactly as it is, no editing the queen's typo 💀)

🐛 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

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🌈 AUTHOR - Sheldon McKay 🌈

email mckays@cshl.edu — shoutout to Sheldon, the author of this whole situation. 💖

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, underscore = backstage pass). 🙈

🧚 new

• Title — new
• Usage — my $seqHandler = Bio::SeqIO::game::seqHandler->new($seq, $ann, $comp, $map, $src )
• Function — constructor method to create a sequence handler
• Returns — a sequence handler object
• Args —
  • $seq — an XML sequence element
  • $ann — a ref. to a list of <annotation> elements
  • $comp — a ref. to a list of <computational_analysis> elements (not used yet)
  • $map — a <map_position> element
  • $src — a flag to indicate that the sequence already has a source feature

🌟 convert

• Title — convert
• Usage — @seqs = $seqHandler->convert
• Function — converts the main XML sequence element and associated annotations to Bio::
• Returns — a ref. to a an array containing the sequence object and a ref. to a list of features
• Args — none

Note — The features and sequence are kept apart to facilitate downstream filtering of features

🎀 _order_feats

• Title — _order_feats
• Usage — $self->_order_feats( $self->{seq_h} )
• Function — an internal method to ensure the source feature comes first and keep gene, mRNA and CDS features together
• Returns — a ref. to an array containing the sequence object and a ref. to a list of features
• Args — a ref. to a hash of sequences

🦋 _add_seq

• Title — _add_seq
• Usage — $self->_add_seq($seq_element)
• Function — an internal method to process the sequence elements
• Returns — nothing
• Args — a sequence element

💅 _map_position

• Title — _map_position
• Usage — $self->_map_position($map_posn_element)
• Function — an internal method to process the <map_position> element
• Returns — nothing
• Args — a map_position element

🍓 _annotation

• Title — _annotation
• Usage — $self->_annotation($annotation_element)
• Function — an internal method to process <annotation> elements
• Returns — nothing
• Args — an annotation element

⭐ _seq

• Title — _seq
• Usage — my $seq = $self->_seq
• Function — an internal sequence getter/setter
• Returns — a Bio::RichSeq object
• Args — a sequence ID

👑 _feat_handler

• Title — _feat_handler
• Usage — my $featHandler = $self->_featHandler
• Function — an internal getter/setter for feature handling objects
• Returns — a Bio::SeqIO::game::featHandler object
• Args — none

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and that's the whole page, bestie!! this one's from perl v5.32.1, dated 2021-08-15 — so like, vintage but still slaying. mwah, bye!! 💋✨🎀