Bio::T...Geneid(3pm)

🌸 NAME 🌸

Bio::Tools::Geneid — the whole vibe is "results of one geneid run" 🧬✨ like it parses one single run of geneid and hands you back the genes, bestie.

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✨ SYNOPSIS ✨

okay so here's the whole group-chat recap of how you'd actually use this:

use Bio::Tools::Geneid;
my $gid = Bio::Tools::Geneid(-file => "geneid.out");

while (my $gene = $gid->next_prediction)
{
  my @transcripts = $gene->transcripts;
    foreach my $t (@transcripts)
    {
      my @exons = $t->exons;
      foreach my $e (@exons)
      {
        printf("Exon %d..%d\n", $e->start, $e->end);
      }
    }
}

look at her go 💅 loops inside loops inside loops, and it's still giving clean.

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🦋 DESCRIPTION 🦋

This is the parser for the output of geneid by Enrique Blanco and Roderic Guigó (IMIM-UPF). 🌈 Go peep http://www1.imim.es/software/geneid if you want the deets.

It relies on the native geneid output format internally, no cap, and it will work with geneid versions 1.0 and 1.1. 🫶

Right now this module only supports the default mode of operation, which is predicting exons and assembling an optimal gene prediction. That's it, that's the whole thing, periodt.

It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object. iconic behavior fr fr 💖

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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. 🥹 seriously, they want to hear from you.

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. 💀 (not me yelling at the maintainer in their DMs, pls)

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. that's the magic combo 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 - Keith James 👑

Email: kdj@sanger.ac.uk

shoutout to Keith, absolute legend, ate and left no crumbs 🎀

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk, underscore = backstage, do not touch unless you know what you're doing. 🙈

🌟 new

Title   : new
Usage   : $obj->new(-file = "<geneid.out");
          $obj->new(-fh => \*GI);
Function: Constructor for geneid wrapper. Takes either a file
        : or filehandle
Returns : L<Bio::Tools::Geneid>

it's the constructor, the main character moment of every object 🌸 hand it a file or a filehandle and it's off.

🌟 next_prediction

Title   : next_prediction
Usage   : while($gene = $geneid->next_prediction)
          {
              # do something
          }
Function: Returns the gene structure prediction of the geneid result
          file. Call this method repeatedly until FALSE is returned.
Returns : A Bio::SeqFeature::Gene::GeneStructure object
Args    : None

call it over and over until it goes FALSE — that's your sign to stop, bestie. 🛑

🌟 _add_exon

Title   : _add_exon
Usage   : $obj->_add_exon($gene, $transcript, ... exon data ...)
Function: Adds a new exon to both gene and transcript from the data
        : supplied as args
Example :
Returns : Nothing

internal method energy 💅 it adds a new exon to both the gene <em>and</em> the transcript, from the data you handed it as args. Returns nothing. silent, mysterious, iconic.

🌟 _set_strand

Title   : _set_strand
Usage   : $obj->_set_strand($gene)
Function: Sets the overall gene strand to the same strand as all
        : the exons if they are all on the same strand, or to strand 0
        : if the exons are on different strands.
Example :
Returns : Nothing

the strand vibe check 🧚 — all exons agree? cool, gene matches them. they're fighting? strand 0, we're not picking sides.

🌟 _target_id

Title   : _target_id
Usage   : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns : A target ID

get/set for the genomic sequence id 🎀 that's it. that's the method. she's simple, she's efficient, she slays.

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and that's the whole page, bestie — go parse some genes 💖

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perl v5.32.1, dated 2021-08-15, from the Bio::T...Geneid(3pm) manual page — mwah, thanks for reading, ily, bye 🫶✨