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

💖 Bio::SeqIO::bsml_sax — the manual, but make it a group chat 💖

okay so bestie, the page you're reading is literally Bio::S...ml_sax(3pm) from the Perl user-contributed docs, and the module living inside it is Bio::SeqIO::bsml_sax — a BSML sequence input/output stream powered by SAX. yes. SAX. the XML one. we're doing this. 🎀

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✨ NAME ✨

Bio::SeqIO::bsml_sax — BSML sequence input/output stream using SAX 🦋

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✨ SYNOPSIS ✨

okay so lowkey? it is probably best not to use this object directly, and instead go through the SeqIO handler system. that's the whole vibe. respect the handler system, she's the main character. 👑

To read a BSML file:

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

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

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

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

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

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

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✨ DEPENDENCIES ✨

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

• XML::SAX — yes she's the whole personality here 💅

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✨ DESCRIPTION ✨

This object can transform Bio::Seq objects to and from BSML (XML) flatfiles. that's it. that's the job. converting your seqs back and forth like the icon she is. 🔥

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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

🫂 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. (also yes, "reponsive" is spelled like that in the original and we're not touching it, periodt. 💀)

🐛 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 - Jason Stajich ✨

Email jason-at-bioperl-dot-org — iconic of him honestly 💜

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✨ METHODS ✨

🔍 next_seq

• Title : next_seq
• Usage : my $bioSeqObj = $stream->next_seq
• Function: Retrieves the next sequence from a SeqIO::bsml stream.
• Returns : A reference to a Bio::Seq::RichSeq object
• Args : (nothing, bestie — zero args, empty plate, clean slate 🌸)

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reminder reminder: do not use this object directly if you can help it. go through the SeqIO handler system. iykyk. 🧚

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and that's the whole page, bestie!! this one came from the Perl user-contributed documentation, page Bio::S...ml_sax(3pm), shipped with perl v5.32.1 and dated 2021-08-15. slay, go read your sequences. 💖✨🌈