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

✨ NAME ✨

ok so this is Bio::T...Genscan(3pm) — it's the module Bio::Tools::Genscan, and it holds the results of one Genscan run. one run, one vibe, one whole gene prediction 💅

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🌸 SYNOPSIS 🌸

bestie, here's the whole flow, no cap:

use Bio::Tools::Genscan;

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

# 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 = $genscan->next_prediction()) {
    # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
    # off Bio::SeqFeature::Gene::Transcript.
    #
    # $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 = $gene->exons('Terminal');
    # singleton exons:
    ($single_exon) = $gene->exons();
}

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

🚨 real talk: that $genscan->close() is essential if you handed it a filename at initialization. skip it and the file just... stays open. forever. sitting there. open. 😭

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💖 DESCRIPTION 💖

so the Genscan module is a parser for Genscan gene structure prediction output. it takes one gene prediction and turns it into a Bio::SeqFeature::Gene::Transcript-derived object. slay.

it also implements the Bio::SeqAnalysisParserI interface, which means you can drop it in wherever an object like that fits 🫶 go check out Bio::SeqAnalysisParserI.

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🦋 FEEDBACK 🦋

🌈 Mailing Lists

user feedback is literally an integral part of the evolution of this and other Bioperl modules — like, the whole thing grows because of y'all 💜 send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, fr fr.

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 so many experienced and reponsive experts who will be able to look at the problem and quickly address it 👑 and pls pls pls include a thorough description of the problem with code and data examples if at all possible — it helps so much.

🍓 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of 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@gmx.net

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⭐ APPENDIX ⭐

the rest of the documentation details each of the object methods, bestie. internal methods are usually preceded with a _ (iykyk 👀).

💜 analysis_method

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

it's inherited, but overridden so the name has to match /genscan/i — case-insensitive, periodt.

🧚 next_feature

Title   : next_feature
Usage   : while($gene = $genscan->next_feature()) {
                 # do something
          }
Function: Returns the next gene structure prediction of the Genscan 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.

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

so you call it over and over until you get FALSE back. what you get is actually a SeqFeatureI implementing object. it's required for classes implementing the SeqAnalysisParserI interface, and rn it's just an alias for next_prediction() — same thing, different name 💫

🌸 next_prediction

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

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

same energy as above: keep calling it until FALSE shows up, and each call hands you a 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 :

it parses the prediction section. next_prediction() calls it automatically if it hasn't happened yet, so you don't gotta worry about it 😌

🫶 _prediction

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

internal. that's it. that's the whole thing 🤫

🌈 _add_prediction

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

also internal 🫣

⭐ _predictions_parsed

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

internal, returns TRUE or FALSE.

🎀 _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

tells you whether or not the result contains the predicted CDSs too 👀 returns TRUE or FALSE.

🦋 _read_fasta_seq

Title   : _read_fasta_seq()
Usage   : ($id,$seqstr) = $obj->_read_fasta_seq();
Function: Simple but specialised FASTA format sequence reader. Uses
          $self->_readline() to retrieve input, and is able to strip off
          the traling description lines.
Example :
Returns : An array of two elements.

a simple but specialised FASTA format sequence reader. it uses $self->_readline() to retrieve input, and it can strip off the traling description lines. returns an array of two elements — ($id,$seqstr), cute 💖

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and that's the whole page, bestie!! you ate this. go parse some genes 🧬✨

💖 this has been Bio::T...Genscan(3pm) from perl v5.32.1, dated 2021-08-15, filed under User Contributed Perl Documentation 💖