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

💖 Bio::T...scanSE(3pm) 💖

okay bestie, buckle up — this is the user-contributed Perl documentation for Bio::Tools::tRNAscanSE, and it's literally the parser that reads your tRNAscan-SE output. no cap. ✨

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🌸 NAME 🌸

Bio::Tools::tRNAscanSE — a parser for tRNAscan-SE output. that's it, that's the whole vibe. 🧚

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✨ SYNOPSIS ✨

the way you just... use it:

use Bio::Tools::tRNAscanSE;

my $parser = Bio::Tools::tRNAscanSE->new(-file => 'result.tRNAscanSE');

# parse the results
while( my $gene = $parser->next_prediction ) {

    @exon_arr = $gene->get_SeqFeatures();

}

look at that. immaculate. 🫶

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🦋 DESCRIPTION 🦋

so this script will parse tRNAscan-SE output. just the tabular output of the tRNA locations in the genome for now — that's the current scope, bestie, don't come for it. 💅

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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 the Bioperl mailing list. 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. 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. (yes, "reponsive" is exactly how it's spelled here — we keep it real. 💀)

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us 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 - 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 _ — you know, the secret menu. 🙈

⭐ new

Title   : new
Usage   : my $obj = Bio::Tools::tRNAscanSE->new();
Function: Builds a new Bio::Tools::tRNAscanSE object
Returns : an instance of Bio::Tools::tRNAscanSE
Args    : -fh/-file for input filename
          -genetag => primary tag used in gene features (default 'tRNA_gene')
          -exontag => primary tag used in exon features (default 'tRNA_exon')
          -srctag  => source tag used in all features (default 'tRNAscan-SE')

this is the moment where you build the whole object. main character energy, honestly. ✨

⭐ gene_tag

Title   : gene_tag
Usage   : $obj->gene_tag($newval)
Function: Get/Set the value used for the 'gene_tag' of genes
          Default is 'tRNA_gene' as set by the global $GeneTag
Returns : value of gene_tag (a scalar)
Args    : on set, new value (a scalar or undef, optional)

⭐ source_tag

Title   : source_tag
Usage   : $obj->source_tag($newval)
Function: Get/Set the value used for the 'source_tag' of exons and genes
          Default is 'tRNAscan-SE' as set by the global $SrcTag
Returns : value of source_tag (a scalar)
Args    : on set, new value (a scalar or undef, optional)

⭐ exon_tag

Title   : exon_tag
Usage   : $obj->exon_tag($newval)
Function: Get/Set the value used for the 'primary_tag' of exons
          Default is 'tRNA_exon' as set by the global $ExonTag
Returns : value of exon_tag (a scalar)
Args    : on set, new value (a scalar or undef, optional)

⭐ analysis_method

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

inherited method, but it got a glow-up — it's overridden so the name matches /tRNAscan-SE/i. 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::SeqFeature::Generic object.
Args    :
See also : L<Bio::SeqFeature::Generic>

heads up bestie: call it repeatedly until FALSE is returned, that's how you know you've hit the end. no infinite looping, okay? 😭

it's literally just an alias for next_prediction() at present — same girl, 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::SeqFeature::Generic object.
Args    :
See also : L<Bio::SeqFeature::Generic>

same deal: call it repeatedly until FALSE is returned. 🍓

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and that's the whole page, bestie!! this was perl v5.32.1, dated 2021-08-15, and yeah the title got truncated to Bio::T...scanSE(3pm) but we know what it really is. slay, go parse some tRNAs. 💜✨