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

✨ NAME ✨

Bio::Tools::Grail — bestie, this is the results of one (1) Grail run 💖 it's a whole Perl module, manual page Bio::T...::Grail(3pm), and she is ready to hand you gene predictions.

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🦋 SYNOPSIS 🦋

$grail = Bio::Tools::Grail->new(-file => 'result.grail');
# filehandle:
$grail = Bio::Tools::Grail->new( -fh  => \*INPUT );

# parse the results
while($gene = $grail->next_prediction()) {
    # $gene is an instance of Bio::Tools::Prediction::Gene

    # $gene->exons() returns an array of
    # Bio::Tools::Prediction::Exon objects
    # all exons:
    @exon_arr = $gene->exons();

    # initial exons only
    @init_exons = $gene->exons('Initial');
    # internal exons only
    @intrl_exons = $gene->exons('Internal');
    # terminal exons only
    @term_exons = $gene->exons('Terminal');
    # singleton exons only -- should be same as $gene->exons() because
    # there are no other exons supposed to exist in this structure
    @single_exons = $gene->exons('Single');
}

# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$genscan->close();

ok so lowkey the whole flow is: make the object, loop next_prediction(), grab those exons, then close() — and yes, that close() is essential if you passed a filename at init, otherwise the file just stays open forever like a group chat you never muted 😭

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🌸 DESCRIPTION 🌸

The Grail module provides a parser for Grail gene structure prediction output. That's the whole vibe. She reads the output, she parses it, she gives you gene structures. Periodt. 👑

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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. 🫶

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.

ngl this is the good part — there are actual experienced, responsive experts on that list and they'll clock your problem fast. Just please bring a thorough description plus your code and data examples, bestie, don't just show up with "it doesn't work" 🙈

🐛 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 - Jason Stajich 👑

Email jason-at-bioperl.org

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

🌟 next_prediction

Title   : next_prediction
Usage   : while($gene = $grail->next_prediction()) {
                 # do something
          }
Function: Returns the next gene structure prediction of the Grail result
          file. Call this method repeatedly until FALSE is returned.

Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args    :

So you just keep calling it and keep calling it until it hands you back FALSE — that's your cue to stop, babe. Each call gives you one Bio::Tools::Prediction::Gene object. ✨

🔍 _parse_predictions

Title   : _parse_predictions()
Usage   : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
          next_prediction() if not yet done.
Example :
Returns :

Parses the prediction section — and good news, next_prediction() calls her automatically if she hasn't been run yet, so you don't gotta babysit her. 🧚

🔮 _prediction

Title   : _prediction()
Usage   : $gene = $obj->_prediction()
Function: internal
Example :
Returns :

internal. that's it, that's the description 💀

➕ _add_prediction

Title   : _add_prediction()
Usage   : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :

also internal, also just doing her little behind-the-scenes thing 💅

✅ _predictions_parsed

Title   : _predictions_parsed
Usage   : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE

internal, and she returns TRUE or FALSE so you can vibe check whether the parsing already happened 🌈

🧬 _has_cds

Title   : _has_cds()
Usage   : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE

Basically: does this result ALSO have the predicted CDSs, or not? Returns TRUE or FALSE. No cap. 🔥

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and that's the whole page, bestie!! 🎀 this was perl v5.32.1, dated 2021-08-15, straight outta the User Contributed Perl Documentation for Bio::T...::Grail(3pm) — go parse some genes, you absolute icon 💖✨🦋