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

💖 NAME 💖

Bio::SeqIO::swissdriver — the SwissProt/UniProt handler-based push parser, bestie. She's a Perl module, she lives in the Bioperl docs, and she's iconic.

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✨ SYNOPSIS ✨

okay so real talk, do not come for this object directly, she's not built for that. go through the SeqIO handler instead:

#It is probably best not to use this object directly, but
#rather go through the SeqIO handler:

$stream = Bio::SeqIO->new(-file => $filename,
                          -format => 'swissdriver');

while ( my $seq = $stream->next_seq() ) {
    # do something with $seq
}

like. that's it. that's the whole vibe. 🦋

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🌸 DESCRIPTION 🌸

This object can transform Bio::Seq objects to and from UniProt flat file databases. slay.

so here's the tea: there's the tried-and-true Bio::SeqIO::swiss parser, and then there's this version. the key difference (no cap) is that this one splits the parsing and the data manipulation into two separate things — a 'driver' method (next_seq) and separate object handlers that deal with the data passed to them. it's giving separation of concerns. it's giving main character energy. 💅

🎀 The Driver 🎀

The main purpose of the driver routine, in this case next_seq(), is to carve out the data into meaningful chunks which are passed along to relevant handlers (see below).

Each chunk of data in the has a NAME tag attached to it, similar to that for XML parsing. This designates the type of data passed (annotation type or seqfeature) and the handler to be called for processing the data. it's literally XML vibes but make it UniProt. 🙈

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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. (yes bestie, they actually want to hear from you, this is not a drill)

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.

okay this part matters: don't dm the maintainer, post to the list. the whole squad is there and they will clock your problem so fast. 👑

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track 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 - Bioperl Project 👑

bioperl-l at bioperl.org

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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 means stay out unless you know what you're doing, bestie)

⭐ next_seq

Title   : next_seq
Usage   : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args    : none

⭐ write_seq

Title   : write_seq
Usage   : $stream->write_seq($seq)
Function: writes the $seq object (must be seq) to the stream
Returns : 1 for success and 0 for error
Args    : array of 1 to n Bio::SeqI objects

⭐ seqhandler

Title   : seqhandler
Usage   : $stream->seqhandler($handler)
Function: Get/Set the Bio::Seq::HandlerBaseI object
Returns : Bio::Seq::HandlerBaseI
Args    : Bio::Seq::HandlerBaseI

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and that's the whole page, bestie. 💜 this one came to you from perl v5.32.1, dated 2021-08-15, and yeah the title got squished to Bio::S...sdriver(3pm) in the header because manpage formatting said so. go forth and parse some UniProt. periodt. 💅✨