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

🌸 NAME 🌸

Bio::SeqIO::entrezgene — the Entrez Gene ASN1 parser, bestie 💖

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✨ VERSION ✨

version 1.73 — yeah she's got a number, she's official 👑

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🫶 SYNOPSIS 🫶

okay so listen, do not go making this one yourself, okay? like literally do not instantiate it directly, use the vibe-approved path:

use Bio::SeqIO;

# don't instantiate directly - instead do
my $seqio = Bio::SeqIO->new(-format => 'entrezgene',
                            -file => $file);
my $gene = $seqio->next_seq;

that's it. that's the whole thing. slay 💅

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🦋 DESCRIPTION 🦋

So this is the EntrezGene ASN bioperl parser, and she is built on top of Bio::ASN1::EntrezGene — which is a low level ASN parser built by Mingyi Liu (<http://sourceforge.net/projects/egparser>). The easiest way to use it? That's literally the code right up there ⬆️. No cap.

You will get most of the Entrez Gene annotation, like gene symbol, gene name and description, accession numbers associated with the gene, etc. And almost all of these are given as Bio::AnnotationI objects. iconic behaviour fr fr 🌈

If you need all the data, do this:

my $seqio = Bio::SeqIO->new(-format => 'entrezgene',
                            -file => $file,
                            -debug => 'on' );
my ($gene,$genestructure,$uncaptured) = $seqio->next_seq;

The second variable returned, $genestructure, is a Bio::Cluster::SequenceFamily object. It contains all Refseqs and the genomic contigs that are associated with the particular gene. The third variable, $uncaptured, is a reference to a plain array. 📦

You can also modify the output to allow back compatibility with the old LocusLink parser:

my $seqio = Bio::SeqIO->new(-format => 'entrezgene',
                            -file => $file,
                            -locuslink => 'convert');

⚠️ heads up bestie: the -debug and -locuslink options slow down the parser. it's giving "worth it but at what cost" 😭

Example code which looks for ontology terms:

my $eio = new Bio::SeqIO(-file => $file,
                         -format => 'entrezgene',
                         -service_record => 'yes');

while (my $seq = $eio->next_seq) {
  my $gid = $seq->accession_number;
  foreach my $ot ($ann->get_Annotations('OntologyTerm')) {
    next if ($ot->term->authority eq 'STS marker'); # No STS markers
    my $evid = $ot->comment;
    $evid =~ s/evidence: //i;
    my @ref = $ot->term->get_references;
    my $id = $ot->identifier;
    my $fid = 'GO:' . sprintf("%07u",$id);
    print join("\t",$gid, $ot->ontology->name, $ot->name, $evid,
      $fid, @ref?$ref[0]->medline:''), "\n";
  }
}

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🧚 _process_products_coordinates 🧚

To do: 🚧 (yes she's a WIP, we love an unfinished icon)

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🎀 _process_prop 🎀

To do: process GO 🚧

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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 the Bioperl mailing list. Your participation is much appreciated 🥹💜

bioperl-l@bioperl.org              - General discussion
http://bioperl.org/Support.html    - 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 detail the better, bestie — give them the whole lore ✍️

🐛 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/bio-asn1-entrezgene/issues

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👑 AUTHOR 👑

Stefan Kirov <skirov@utk.edu> — thank you for your service 🫡💖

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⭐ COPYRIGHT ⭐

This software is copyright (c) by Stefan Kirov <skirov@utk.edu>.

This software is available under the same terms as the perl 5 programming language system itself.

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and that's the whole page, bestie!! 🎀 this was perl v5.38.2, dated 2024-03-04, from Bio::S...ezgene(3pm) — User Contributed Perl Documentation. mwah, go parse some genes, ilysm 💅✨🦋