Bio::F...ctoryI(3pm)

💖 Bio::Factory::SequenceFactoryI 💖

okay so bestie, this is a page from the User Contributed Perl Documentation — yes it's giving official-but-make-it-fandom, and yes it's a Perl module doc. We're looking at Bio::Factory::SequenceFactoryI(3pm) and I'm gonna walk you through it like we're texting at 2am. 🫶

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✨ NAME ✨

Bio::Factory::SequenceFactoryI — this is the interface that lets you build sequences in a generic way inside factories that make sequences (like SeqIO). Think of it as the vibe contract everyone agrees to. 💅

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✨ SYNOPSIS ✨

okay first thing's first, the doc is literally screaming at us:

# do not use this object directly it is an interface
# get a Bio::Factory::SequenceFactoryI object like

so like. don't touch it directly, it's an interface, it's not the moment. Instead you get a Bio::Factory::SequenceFactoryI object like this:

use Bio::Seq::SeqFactory;
my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::PrimarySeq');

my $seq = $seqbuilder->create(-seq => 'ACTGAT',
                              -display_id => 'exampleseq');

print "seq is a ", ref($seq), "\n";

look at that. iconic. ✨ the builder builds, the sequence gets a -display_id, and we print out what kind of thing it is. main character energy fr fr. 👑

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✨ DESCRIPTION ✨

So the whole point here is a generic way to build Sequence objects via a pluggable factory. And bestie, why do we care? Because it cuts down on code that looks like this absolute nightmare:

if( $type  eq 'Bio::PrimarySeq' ) { ... }
elsif( $type eq 'Bio::Seq::RichSeq' ) { ... }

like... the endless if-elsif chain? no. we're not doing that. the factory handles it. slay. 💀✨

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✨ FEEDBACK ✨

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. So send your comments and suggestions, preferably to the Bioperl mailing list. Your participation is much appreciated — like genuinely, 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

and NOT to the module maintainer directly. Why? Because there are many experienced and responsive experts who will be able to look at the problem and quickly address it. (the original says "reponsive" btw — typo and all, we're keeping it, no cap 😭)

Please include a thorough description of the problem with code and data examples if at all possible. give them the whole lore, not just the teaser. 📖

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so they can 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 - Jason Stajich ✨

Email: jason-at-bioperl.org — shoutout to Jason, the author, the blueprint, the moment. 🌟

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✨ APPENDIX ✨

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — so if you see an underscore, that's an inside-thought, not for you bestie. 🙈

🌸 create

Title   : create
Usage   : my $seq = $seqbuilder->create(-seq => 'CAGT',
                                        -id => 'name');
Function: Instantiates new Bio::PrimarySeqI (or one of its child classes)
          This object allows us to genericize the instantiation of sequence
          objects.
Returns : Bio::PrimarySeqI
Args    : initialization parameters specific to the type of sequence
          object we want.  Typically
          -seq        => $str,
          -display_id => $name

so create instantiates a new Bio::PrimarySeqI (or one of its child classes), and it's literally the whole reason this object exists — to genericize the instantiation of sequence objects. It returns a Bio::PrimarySeqI, and the args are initialization params specific to whatever kind of sequence object you want. Typically -seq with your string and -display_id with your name. that's it. that's the method. 💖

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and that's the whole page bestie!! this was Bio::Factory::SequenceFactoryI(3pm) from the User Contributed Perl Documentation, running on perl v5.32.1 and dated 2021-08-15. go forth and build your sequences generically, you absolute legend. 🦋✨💅 periodt.