Bio::SeqIO::game(3pm)

💖 NAME 💖

okay bestie, so this is Bio::SeqIO::game(3pm) — the user-contributed Perl documentation for it — and it's literally a class for parsing and writing game-XML. that's the whole vibe. parsing. writing. game-XML. periodt. ✨

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🌸 SYNOPSIS 🌸

okay so listen — this module is not used directly, use SeqIO. like, don't come for it directly, that's not the move, iykyk.

use Bio::SeqIO;

my $in = Bio::SeqIO->new ( -file    => 'file.xml',
                           -format  =>  'game',
                           -verbose => 1 );

my $seq = $in->next_seq;

see how we go through Bio::SeqIO? that's the main character. we're just the supporting role 💅

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🦋 DESCRIPTION 🦋

so Bio::SeqIO::game will parse game XML (version 1.2) or write game XML from a Bio::SeqI implementing object. and the XML? it's readable by the genome annotation editor 'Apollo' (www.gmod.org). iconic.

⚠️ but bestie, heads up: it is not backwards compatible with the previous version of game XML. no cap. the old format and this one do NOT talk. 💀

also the XML format currently used by Apollo contains a single 'main' annotated sequence, so we will only get a single annotated sequence in the stream when parsing a game-XML record. one sequence. one stream. that's the situation. 🫶

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💜 FEEDBACK 💜

🌈 Mailing Lists

okay so 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. it's giving community. 🥹

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🎀 Support

bestie, please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. because listen — many experienced and reponsive experts will be able look at the problem and quickly address it. the group chat is stronger than the dm, always. ✨

and please include a thorough description of the problem with code and data examples if at all possible. receipts matter, babe. 📝

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. we're tracking, we're resolving, we're slaying.

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 — the author himself. we stan. 🫡

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⭐ APPENDIX ⭐

the rest of the documentation details each of the object methods. and internal methods? they're usually preceded with a _, so if you see an underscore, mind your business, that's private energy. 🙈

🔥 next_seq

Title   : next_seq
Usage   : my $seq = $seqio->next_seq;
Function: get the main sequence object
Returns : a Bio::Seq::RichSeq object
Args    : none

🔥 write_seq

Title   : write_seq
Usage   : $seqio->write_seq($seq)
Function: writes a sequence object as game XML
Returns : nothing
Args    : a Bio::SeqI compliant object

🧚 _getseqs

Title   : _getseqs
Usage   : $self->_getseqs
Function: An internal method to invoke the PerlSAX XML handler and get
          the sequence objects
Returns : an reference to an array with sequence object and annotations
Args    : none

🧚 _hide_dna

Title   : _hide_dna
Usage   : $seqio->_hide_dna
Function: Hide the DNA for really huge sequences
Returns : nothing
Args    : none

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and that's the page bestie!! this one shipped with perl v5.32.1, dated 2021-08-15, and it's the Bio::SeqIO::game(3pm) manual through and through. go parse something cute. mwah 💖🎀🦋✨