Bio::Tools::MZEF(3pm)

💖 Bio::Tools::MZEF 💖

okay bestie, so this is the manual page for Bio::Tools::MZEF — a lil Perl module that lives in the User Contributed Perl Documentation, and it's literally just "Results of one MZEF run." One run. That's the whole vibe. 🧚

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✨ NAME ✨

Bio::Tools::MZEF — Results of one MZEF run 🎀

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🌸 SYNOPSIS 🌸

no cap, here's the whole flow, copy-paste ready:

$mzef = Bio::Tools::MZEF->new(-file => 'result.mzef');
# filehandle:
$mzef = Bio::Tools::MZEF->new( -fh  => \*INPUT );
# to indicate that the sequence was reversed prior to feeding it to MZEF
# and that you want to have this reflected in the strand() attribute of
# the exons, as well have the coordinates translated to the non-reversed
# sequence
$mzef = Bio::Tools::MZEF->new( -file   => 'result.mzef',
                               -strand => -1 );

# parse the results
# note: this class is-a Bio::Tools::AnalysisResult which implements
# Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
while($gene = $mzef->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();

    # internal exons only
    @intrl_exons = $gene->exons('Internal');
    # note that presently MZEF predicts only internal exons!
}

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

🚨 bestie do NOT forget that $mzef->close() at the end if you handed it a filename when you initialized it — otherwise the file just... stays open. lingering. unhinged. 😭

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🦋 DESCRIPTION 🦋

The MZEF module is a parser for MZEF gene structure prediction output. That's the whole job and it does it. 💅

It inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI. slay.

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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. 🫶 (yes, your little comment really does matter, iykyk)

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. There are lots of experienced and reponsive experts who 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. (translation: give them the receipts, not just "it broke" 🙈)

🐛 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 - Hilmar Lapp 👑

Email hlapp-at-gmx.net (or hilmar.lapp-at-pharma.novartis.com)

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (so if you see an underscore, that's the secret menu, bestie 🌈).

🌟 analysis_method

Usage     : $mzef->analysis_method();
Purpose   : Inherited method. Overridden to ensure that the name matches
            /mzef/i.
Returns   : String
Argument  : n/a

🌟 next_feature

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

          The returned object is actually a SeqFeatureI implementing object.
          This method is required for classes implementing the
          SeqAnalysisParserI interface, and is merely an alias for
          next_prediction() at present.

          Note that with the present version of MZEF there will only be one
          object returned, because MZEF does not predict individual genes
          but just potential internal exons.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args    :

fr fr, only one object comes back with this version of MZEF, because MZEF doesn't predict individual genes — it just predicts potential internal exons. 💀

🌟 next_prediction

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

          Note that with the present version of MZEF there will only be one
          object returned, because MZEF does not predict individual genes
          but just potential internal exons.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args    :

🌟 _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 :

🌟 _prediction

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

🌟 _add_prediction

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

🌟 _predictions_parsed

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

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and that's the whole page, babe 🎀 this one's perl v5.32.1, dated 2021-08-15, straight from Bio::Tools::MZEF(3pm) in the User Contributed Perl Documentation. go parse some exons, you absolute icon 💅✨🦋