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

💖 Bio::SeqIO::gbxml 💖

okay bestie, so this is Bio::SeqIO::gbxml — the GenBank sequence input/output stream that runs on SAX. yes, that SAX. the XML one. not the jazz one. 🎷✨

She ships as part of User Contributed Perl Documentation, and she's here to let you read and write GenBank XML like it's nothing. iykyk. 🦋

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🌸 NAME 🌸

Bio::SeqIO::gbxml — GenBank sequence input/output stream using SAX. that's it. that's the whole vibe. 👑

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✨ SYNOPSIS ✨

ngl, the docs are very clear about this one: it is probably best not to use this object directly, but rather go through the SeqIO handler system. so like, don't text the object directly, go through the group chat. 🫶

To read a GenBank XML file:

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

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

To write a Seq object to the current file handle in GenBank XML format:

$stream->write_seq( -seq => $seqObj);

If instead you would like a XML::DOM object containing the GBXML, use:

my $newXmlObject = $stream->to_bsml( -seq => $seqObj);

that last one? iconic. she doesn't just give you a stream, she gives you a whole DOM. 💅

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🎀 DEPENDENCIES 🎀

In addition to parts of the Bio:: hierarchy, this module uses:

• XML::SAX

just the one extra bestie. low maintenance queen. 🍓

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💜 DESCRIPTION 💜

This object can transform Bio::Seq objects to and from GenBank XML flatfiles. both directions. she's versatile like that. 🔥

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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. fr fr, they mean it. 😭💖

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

🐛 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

not me asking you to file a bug report... but yes. please. do it for the girls. 🙈

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👑 AUTHOR - Ryan Golhar 👑

Email golharam-at-umdnj-dot-edu

(the -at- and -dot- are there to keep the bots from eating the address, we love a cautious queen 🌸)

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⭐ METHODS ⭐

🌈 next_seq

• Title — next_seq
• Usage — my $bioSeqObj = $stream->next_seq
• Function — Retrieves the next sequence from a SeqIO::gbxml stream.
• Returns — A reference to a Bio::Seq::RichSeq object
• Args — (nothing, she takes no arguments, she's mysterious like that) 💅

main character method honestly. you call her, she hands you the next sequence, no drama. slay. ✨🦋

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quick reminder bestie: you still gotta go through the SeqIO handler system — direct use is the "probably best not to" zone. 🎀

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and that's the whole page, no cap. written by Ryan Golhar, shipped as part of User Contributed Perl Documentation for perl v5.32.1 on 2021-08-15. go forth and parse your GenBank XML, you absolute icon. 🧚💜💖