Bio::SeqIO::kegg(3pm)

🦋 Bio::SeqIO::kegg 🦋

okay so bestie, you found Bio::SeqIO::kegg(3pm) — it's part of the User Contributed Perl Documentation and it's literally the KEGG sequence input/output stream. let's get into it 💅

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✨ NAME ✨

Bio::SeqIO::kegg — KEGG sequence input/output stream 🌸

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🎀 SYNOPSIS 🎀

ngl, it's probably best not to use this object directly, but rather go through the SeqIO handler system. so do this:

use Bio::SeqIO;

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

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

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💖 DESCRIPTION 💖

this class transforms KEGG gene records into Bio::Seq objects. periodt.

🌈 Mapping of record properties to object properties 🌈

this section is supposed to document which sections and properties of a KEGG databank record end up where in the Bioperl object model. it is far from complete and presently focuses only on those mappings which may be non-obvious. $seq in the text refers to the Bio::Seq::RichSeqI implementing object returned by the parser for each record. iykyk 🫶

• 'ENTRY' — maps to $seq->primary_id
• 'NAME' — maps to $seq->display_id
• 'DEFINITION' — maps to $seq->annotation->get_Annotations('description');
• 'ORTHOLOG' — maps to grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink')
• 'CLASS' — maps to:

grep {$_->database eq 'PATH'}
         $seq->annotation->get_Annotations('dblink')

• 'POSITION' — FIXME, NOT IMPLEMENTED 😭
• 'PATHWAY' — maps to:

for my $pathway ( $seq->annotation->get_Annotations('pathway') ) {
   #
}

• 'DBLINKS' — maps to $seq->annotation->get_Annotations('dblink')
• 'CODON_USAGE' — FIXME, NOT IMPLEMENTED 😭
• 'AASEQ' — maps to $seq->translate->seq
• 'NTSEQ' — maps to $seq->seq

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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 🥺

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. the more deets the better bestie 💜

🐛 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 - Allen Day 👑

Email allenday@ucla.edu ✨

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📎 APPENDIX 📎

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ 💀

⭐ next_seq ⭐

• Title : next_seq
• Usage : $seq = $stream->next_seq()
• Function: returns the next sequence in the stream
• Returns : Bio::Seq::RichSeq object
• Args :

🌸 write_seq 🌸

• Title : write_seq
• Note : write_seq() is not implemented for KEGG format output. so don't come for me, it's just not a thing 🙈

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and that's the whole vibe, bestie 🎀 this was perl v5.32.1, dated 2021-08-15, and that's a wrap — slay, go parse some KEGG records 💖✨🦋