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

💖 Bio::Tools::Genewise 💖

okay bestie, so this is a perl man page from section 3pm, filed under User Contributed Perl Documentation, and it's literally all about the Bio::Tools::Genewise module. she's giving "results of one Genewise run" energy and honestly? iconic. let's get into it 🧚

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✨ NAME ✨

Bio::Tools::Genewise — the results of one single Genewise run, parsed and served up cute 💅

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🌸 SYNOPSIS 🌸

the vibe check:

use Bio::Tools::Genewise;
my $gw = Bio::Tools::Genewise(-file=>"genewise.out");

while (my $gene = $gw->next_prediction){
  my @transcripts = $gene->transcripts;
    foreach my $t(@transcripts){
      my @exons =  $t->exons;
      foreach my $e(@exons){
          print $e->start." ".$e->end."\n";
      }
    }
}

like, you open a file, you loop the predictions, you loop the transcripts, you loop the exons, and you print the starts and ends. nested loops but make it fashion ✨

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🦋 DESCRIPTION 🦋

so basically this is the parser for the output of Genewise. you hand her either a file handle or a file name (she's flexible, she contains multitudes 💅) and she hands you back a Bio::SeqFeature::Gene::GeneStructure object. that's the whole thing. that's the assignment. she ate. 🔥

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

user feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. 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 (bestie, respect the boundaries 😭). 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 — the more receipts the better 📎

🐛 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 - Fugu Team, Jason Stajich 👑

Email: fugui@worf.fugu-sg.org
Email: jason-at-bioperl.org

the way these two carried this whole module 💀 legends, actually

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk — underscore means not your business, bestie 🙈).

🎀 new 🎀

Title   : new
Usage   : $obj->new(-file=>"genewise.out");
          $obj->new(-fh=>\*GW);
Function: Constructor for genewise wrapper. Takes either a file or filehandle
Example :
Returns : Bio::Tools::Genewise object

she's the constructor for the genewise wrapper and she takes either a file or a filehandle. your girl is not picky 💅

See Bio::Tools::Genewise

🧵 _get_strand 🧵

Title   : _get_strand
Usage   : $obj->_get_strand
Function: takes start and end values, swap them if start>end and
          returns end
Example :
Returns :$start,$end,$strand

takes start and end values, swaps them if start>end, and returns end. little flip moment ✨

⭐ _score ⭐

Title   : _score
Usage   : $obj->_score
Function: get/set for score info
Returns : a score value

get/set for score info. returns a score value. that's it, that's the method 🍓

🧬 _prot_id 🧬

Title   : _prot_id
Usage   : $obj->_prot_id
Function: get/set for protein id
Returns :a protein id

get/set for protein id, and it returns a protein id. consistent queen 💅

🌈 _target_id 🌈

Title   : _target_id
Usage   : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns :a target id

get/set for genomic sequence id, returns a target id.

🔮 next_prediction 🔮

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

Example :
Returns : a Bio::SeqFeature::Gene::GeneStructure object
Args    :

returns the gene structure prediction of the Genewise result file. call this method repeatedly until FALSE is returned — like a while loop, bestie, not a one-and-done. keep calling until she says no 💖

See Bio::SeqFeature::Gene::GeneStructure

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and that's the whole page, no notes 🫶

this lil beauty came to you courtesy of perl v5.32.1, dated 2021-08-15, and it's filed under the section 3pm manual, Bio::Tools::Genewise(3pm). stay parsed, bestie 💜✨