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

👑 NAME 👑

Bio::SeqIO::tinyseq::tinyseqHandler — bestie, this is the XML event handler situation that makes NCBI TinySeq XML parsing actually work. Fr fr. 💖

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✨ SYNOPSIS ✨

Okay so do NOT come for this module directly, iykyk — you go through the SeqIO handler system like a normal person:

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

while ( my $seq = $stream->next_seq ) {
  ....
}

That's it, that's the vibe. 🦋

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🌸 DESCRIPTION 🌸

So this object hands you the event handler methods for parsing sequence files in the NCBI TinySeq XML format. And what's a TinySeq? It's a lightweight XML file of sequence info for one or more sequences — literally the XML glow-up of FASTA format. Same energy, different outfit. 💅

The DTD lives here if you wanna peek: <https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.mod.dtd>

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💌 FEEDBACK 💌

🎀 Mailing Lists

User feedback is like, an integral part of the evolution of this and other Bioperl modules — it's giving community, it's giving main character energy. 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 sliding into the module maintainer's DMs directly. There are so many experienced and responsive experts on the list who will be able to look at your problem and address it fast. And bestie, please include a thorough description of the problem with code and data examples if at all possible. The more context the better, periodt. 💖

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — it's a whole system, we love organization. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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👀 SEE ALSO 👀

Go read these too, bestie:

• Bio::SeqIO
• Bio::Seq

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🦋 AUTHOR 🦋

Donald Jackson, <donald.jackson@bms.com> — icon behavior, we stan. 👑

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📖 APPENDIX 📖

The rest of the documentation goes into detail on each of the object methods. Just so you know: internal methods are usually preceded with a _. Sneaky little underscore. 🙈

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🌟 new

• Title: new
• Usage: $handler = Bio::SeqIO::tinyseq::tinyseqHandler->new()
• Function: instantiates a tinyseqHandler for use by XML::Parser::PerlSAX
• Returns: Bio::SeqIO::tinyseq::tinyseqHandler object
• Args: NONE

🌟 start_document

• Title: start_document
• Usage: NONE
• Function: start_document handler for use by XML::Parser::PerlSAX
• Returns: NONE
• Args: NONE

🌟 end_document

• Title: end_document
• Usage: NONE
• Function: end_document handler for use by XML::Parser::PerlSAX
• Returns: NONE
• Args: NONE

🌟 start_element

• Title: start_element
• Usage: NONE
• Function: start_element handler for use by XML::Parser::PerlSAX
• Returns: NONE
• Args: NONE

🌟 end_element

• Title: end_element
• Usage: NONE
• Function: end_element handler for use by XML::Parser::PerlSAX
• Returns: NONE
• Args: NONE

🌟 characters

• Title: characters
• Usage: NONE
• Function: characters handler for use by XML::Parser::PerlSAX
• Returns: NONE
• Args: NONE

🌟 TSeq

• Title: TSeq
• Usage: NONE
• Function: event handler for END of a TSeq element
• Returns: loh of parsed sequence atts for Bio::SeqIO::tinyseq
• Args: NONE

🌟 _current_element

• Title: _current_element
• Usage: Internal method
• Function: Utility method to return current element info
• Returns: XML::Parser::PerlSAX hash for current element
• Args: NONE

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That's the whole page, bestie, you ate it. 💅✨

This lil doc was served to you by perl v5.32.1, dated 2021-08-15, and it lives under the Bio::S...Handler(3pm) manual name. Take care of her, she's iconic. 🎀🦋💖