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

👑 Bio::Tools::Pseudowise 💅

okay bestie, so this is a page from the User Contributed Perl Documentation collection (the 3pm girlies know), and today we're talking about Bio::Tools::Pseudowise — literally the parser for one single Pseudowise run. no cap.

---

✨ NAME ✨

Bio::Tools::Pseudowise — the results of one Pseudowise run. one. singular. that's the vibe. 🎀

---

🌸 SYNOPSIS 🌸

here's the whole moment, verbatim, do not touch:

use Bio::Tools::Pseudowise;

my $parser = Bio::Tools::Pseudowise->new(-file=>"pw.out");
while(my $feat = $parser->next_result){
    push @feat, $feat;
}

see how she eats? parser in, features out, while loop doing its little dance. iconic. ✨

---

🦋 DESCRIPTION 🦋

so Pseudowise is a pseudogene prediction program — written by Ewan Birney as part of the Wise Package, we love a legend — and this module right here is the parser for the output of that program. it's giving translator. it's giving interpreter of vibes. 🫶

http://www.sanger.ac.uk/software/wise2

---

💖 FEEDBACK 💖

🌈 Mailing Lists

bestie, user feedback is an integral part of the evolution of this module and every other Bioperl module. it literally is. so send your comments and suggestions to one of the Bioperl mailing lists — your participation is so appreciated, fr fr.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🌸 Support

okay so listen: please direct your usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

and not to the module maintainer directly, okay? not the main character DM, the group chat. there are so many experienced and responsive experts on there who will look at your problem and quickly address it. and if you can, please include a thorough description of the problem with code and data examples. give them the full lore. 🙈

💀 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. it's a whole thing. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

---

👑 AUTHOR - Jason Stajich 👑

• Previously committed by the Fugu Team
• Re-written by Jason Stajich jason-at-bioperl-dot-org

---

🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — you know, the secret menu. iykyk. 🧚

⭐ analysis_method

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

inherited but overridden, so the name has to match /pseudowise/i — case-insensitive, she's flexible but she has standards. 💅

⭐ next_feature

Title   : next_feature
Usage   : $seqfeature = $obj->next_feature();
Function: Returns the next feature available in the analysis result, or
          undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
          more features.
Args    : none

See Also Bio::SeqFeatureI

⭐ next_prediction

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

Example :
Returns : a Bio::SeqFeature::Generic
Args    : none

See Also Bio::SeqFeature::Generic

call it over and over until it goes FALSE — that's the whole loop, that's the whole relationship. 💜

⭐ _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 :

she parses the prediction section for you automatically, no need to micromanage her. 💅

⭐ _prediction

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

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

⭐ _add_prediction

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

also internal, also mysterious, also slaying quietly. ✨

⭐ _predictions_parsed

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

internal, but she will tell you TRUE or FALSE. a truth-teller. 🌈

---

so yeah, that's the whole page, bestie. 💖 this little gem lives in perl v5.32.1, dated 2021-08-15, and it's filed under Bio::T...dowise(3pm) — the abbreviation is a whole mood, honestly. go forth, parse your pseudogenes, and stay iconic. periodt. 👑✨