Bio::G...helper(3pm)

💖 Bio::G...helper(3pm) 💖

okay bestie, gather round — this is the User Contributed Perl Documentation page for Bio::Graphics::Browser2::GFFhelper, and yes the name got truncated to Bio::G...helper like it's hiding its government name. We know her. She helps gbrowse plugins handle GFF. Let's get into it. 🦋

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✨ NAME ✨

Bio::Graphics::Browser2::GFFhelper — Helps gbrowse plugins handle GFF 💅

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🌸 SYNOPSIS 🌸

  package Bio::Graphics::Browser2::Plugin::MyPlugin;

  use vars qw/@ISA $ROLLBACK/;

  @ISA = qw/ Bio::Graphics::Browser2::Plugin
             Bio::Graphics::Browser2::GFFhelper /;

  $ROLLBACK = '/tmp/';

  # other plugin subs skipped...

  sub save_segment {
    my ($self, $segment) = @_;
    return 0 unless $ROLLBACK;
    $self->{rb_loc} ||= $ROLLBACK;
    $self->save_state($segment);
    1;
  }

  sub gff_from_rollback {
    my $self = shift;
    my $conf = $self->configuration;

    # don't save a persistent rb_id, look for a CGI param each time
    my $rollback = $self->config_param('rb_id');

    my $gff = $self->rollback($rollback);

    # this is a rollback to an earlier version of an existing segment
    # we don't need DNA, just the GFF
    $gff;
  }

  # read GFF2 dialects
  sub gff {
    my $self = shift;
    my $gff  = shift;

    # set a flag to add a header to the GFF
    $self->{header} = 1;

    # set sequence name in case the GFF does not have it
    $self->refseq('L16622');

    # process the GFF, convert it to GFF3, get the sequence
    my ($newGFF, $dna) = $self->read_gff($gff);
    return ($newGFF, $dna);
  }

literally the whole vibe right there in one block, no notes 💜

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🎀 DESCRIPTION 🎀

This module helps process GFF prior to loading into the database and provides rollback capability for feature editors/loaders. Like a lil backstage crew making sure everything looks right before it goes on stage. 🔥

🧬 GFF help 🧬

This module deals with the different GFF2 dialects and changes them to GFF3 format. It also lets you convert Bio::DB::GFF::Feature objects into Bio::SeqFeature::Generic objects — which is required for consistent feature and attribute handling across different input/output formats. No cap, it's the glow-up your features needed. ✨

🐚 Sequence Extraction 🐚

If DNA is appended to the GFF, it will be extracted. The read_gff method returns a string containing processed GFF and also a sequence string. Two for one, bestie. 🫶

⏪ Rollbacks ⏪

The state of a segment can be captured and saved in case the user wants to revert to an earlier version of the segment after editing/deleting features. Like a save point before you do something chaotic. 😭

The last 10 modified segments are saved in a round-robin rotation. 🔁

In plugins that inherit methods from this module, the $ROLLBACK variable must be defined with a string containing the path to a directory where the web user (apache, nobody, etc.) has write access.

⚠️ If $ROLLBACK is undefined, the rollback functionality is disabled. So set it or lose it, fr fr. 💀

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📣 FEEDBACK 📣

See the GMOD website for information on bug submission http://www.gmod.org 🐛✨

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👑 AUTHOR - Sheldon McKay 👑

Email smckay@bcgsc.bc.ca 📧

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty. 📜

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and that's the whole page bestie, served up fresh from perl v5.40.0, dated 2024-10-20 💖 stay iconic, go read your GFF, mwah 🎀✨🦋