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

💖 Bio::SeqIO::embldriver — EMBL sequence input/output stream 💖

okay bestie, so this is the manual page for Bio::SeqIO::embldriver, which lives in the User Contributed Perl Documentation section of the perl man pages (that's the 3pm vibe, iykyk). Buckle up, it's giving bioinformatics realness. 🧬✨

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✨ NAME ✨

Bio::SeqIO::embldriver — an EMBL sequence input/output stream. That's it, that's the whole name. 💅

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🌸 SYNOPSIS 🌸

ngl bestie, it's probably best not to use this object directly?? like, go through the SeqIO handler system instead, it's so much cuter. Do this:

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

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

slay. that's the whole flow. 🦋

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💜 DESCRIPTION 💜

This object can transform Bio::Seq objects to and from EMBL flat file databases. iconic behaviour fr.

There is a lot of flexibility here about how to dump things, which should be documented more fully. (not me calling out the docs 💀)

There should be a common object that this and Genbank share (probably with Swissprot too). Too much of the magic is identical — lowkey redundant, highkey relatable. 🙈

🎀 Optional functions 🎀

• _show_dna() — (output only) shows the dna or not. yes bestie, dna visibility toggle.
• _post_sort() — (output only) provides a sorting func which is applied to the FTHelpers before printing. sort before you serve, periodt.
• _id_generation_func() — this is a function which is called as:

print "ID   ", $func($annseq), "\n";

To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools. ✨

If you want to output annotations in EMBL format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method annotation(). 🫶

The following are the names of the keys which are polled from a Bio::Annotation::Collection object:

• reference — should contain Bio::Annotation::Reference objects
• comment — should contain Bio::Annotation::Comment objects
• dblink — should contain Bio::Annotation::DBLink objects

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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. (they literally want to hear from you bestie, don't be shy 💌)

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, the original says "reponsive" — typo and all, we keep it 💀)

🐛 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 - Ewan Birney 👑

Email birney@ebi.ac.uk — the main character who wrote this. 🎀

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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 "not your business, bestie, but here's the tea anyway")

⭐ next_seq

• Title — next_seq
• Usage — $seq = $stream->next_seq()
• Function — returns the next sequence in the stream
• Returns — Bio::Seq object
• Args — (nothing, she takes no args)

⭐ 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, no notes. 🦋✨ this was perl v5.32.1, dated 2021-08-15, straight from the User Contributed Perl Documentation files. go forth and EMBL, you absolute icon 💅🌈💖