Bio::D...r::seq(3pm)

✨ NAME ✨

Bio::DB::SoapEUtilities::FetchAdaptor::seq — bestie, this is the fetch adaptor for 'seq' efetch SOAP messages 💅 it's the whole reason your sequences show up looking all cute and parsed.

(yes this is the manual page for Bio::D...r::seq(3pm), we're doing this, buckle up 🎀)

---

🌸 SYNOPSIS 🌸

Imported by Bio::DB::SoapEUtilities::FetchAdaptor as required. That's it, that's the whole synopsis, she's a behind-the-scenes queen 👑

---

🦋 DESCRIPTION 🦋

Okay so what this actually does: it hands you back an iterator over either Bio::Seq or Bio::Seq::RichSeq objects — which one you get depends entirely on the return type of the efetch. Vibe check on that: it's giving "same method, different era" ✨

A standard efetch to a sequence database returns a GenBank SOAP result, and that gets parsed into rich sequence objects (the fancy ones, the main characters 💖):

my $fac = Bio::DB::SoapEUtilities->new;
my $seqio = $fac->efetch(-db => 'protein', -id => 730439)->run(-auto_adapt=>1);
my $seq = $seqio->next_seq;
$seq->species->binomial; # returns 'Bacillus caldolyticus'

But an efetch with -rettype => 'fasta'? That gets parsed into plain Bio::Seq objects instead — and ngl, it's VERY much faster 🔥 like, speed demon behaviour:

$seqio = $fac->efetch( -rettype => 'fasta' )->run(-auto_adapt=>1);
$seq = $seqio->next_seq;
$seq->species; # undef
$seq->desc; # kitchen sink

Notice that $seq->species is undef there and $seq->desc is just... the kitchen sink. The fast path trades the fancy metadata for zoom. Pick your fighter 💀

And if you're ever sitting there like "wait, which one did I even get??" — to find out the object type returned:

$class = $seqio->obj_class;

...exactly like it works for all Bio::DB::SoapEUtilities::FetchAdaptor objects. Consistency, we love her 🫶

---

👑 SEE ALSO 👑

• Bio::DB::SoapEUtilities
• Bio::DB::SoapEUtilities::FetchAdaptor

---

💌 FEEDBACK 💌

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, your thoughts are the moment 🌟 Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated, no cap 🙏

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. Because there are so many experienced and reponsive experts hanging out there who will be able to 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 — receipts help, always 🧾✨

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:

http://redmine.open-bio.org/projects/bioperl/

---

🎀 AUTHOR - Mark A. Jensen 🎀

Email: maj -at- fortinbras -dot- us 📧

---

🌈 CONTRIBUTORS 🌈

Much inspiration from Bio::SeqIO and family. Shoutout to the whole family tree, they ate 🍽️

---

⭐ APPENDIX ⭐

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk, the underscore ones are the private besties, don't @ them 🙈).

---

And that's the whole page, bestie!! This one's from the Perl v5.36.0 era, dated 2023-01-22, and it lives under the Bio::D...r::seq(3pm) name. Go get your sequences, you absolute icon 💖✨🦋