Bio::S...O::wise(3pm)

💖 Bio::S...O::wise — bestie edition 💖

okay so this is the manual page for Bio::S...O::wise, a lil Perl module that lives in the Bioperl world, and it's filed under the 3pm section (that's Perl module docs, iykyk). Sit down, grab a boba, we're parsing Wise output together 🧋✨

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✨ NAME ✨

Bio::SearchIO::wise — Parsing of wise output as alignments 🦋

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🌸 SYNOPSIS 🌸

the vibe, in code:

use Bio::SearchIO;
my $parser = Bio::SearchIO->new(-file    => 'file.genewise',
                               -format  => 'wise',
                               -wisetype=> 'genewise');

while( my $result = $parser->next_result ) {}

like, you make a Bio::SearchIO, you tell it -format => 'wise', you tell it which flavor of wise with -wisetype, and then you just loop on next_result until there's nothing left. slay 💅

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🫶 DESCRIPTION 🫶

This object parsers Wise output using Bio::Tools::Genewise or Bio::Tools::Genomewise as a helper. ✨ (yes bestie, the original really does say "parsers" — we keep the facts exactly as they are, always 👑)

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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, they mean it 🥺

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.

no cap: skip the maintainer's DMs, go to the list, and bring receipts — code + data examples 💖

🐛 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-dot-org 💜

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🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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🧚 new

Title   : new
Usage   : my $obj = Bio::SearchIO::wise->new();
Function: Builds a new Bio::SearchIO::wise object
Returns : an instance of Bio::SearchIO::wise
Args    : -wise => a Bio::Tools::Genewise or Bio::Tools::Genomewise object

building the whole thing from scratch, main character energy ⭐

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🦋 next_result

Title   : next_result
Usage   : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args    : none

no args, just vibes 🍓

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💅 start_element

Title   : start_element
Usage   : $eventgenerator->start_element
Function: Handles a start element event
Returns : none
Args    : hashref with at least 2 keys 'Data' and 'Name'

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💅 end_element

Title   : start_element
Usage   : $eventgenerator->end_element
Function: Handles an end element event
Returns : none
Args    : hashref with at least 2 keys 'Data' and 'Name'

not me pointing out that the Title here says start_element in the original — we do NOT fix it, we report it exactly, periodt 🙈

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💅 element

Title   : element
Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convience method that calls start_element, characters, end_element
Returns : none
Args    : Hash ref with the keys 'Name' and 'Data'

(yes, "Convience" — original spelling, keeping it, no notes 💖)

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💅 characters

Title   : characters
Usage   : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args    : string

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🔥 within_element

Title   : within_element
Usage   : if( $eventgenerator->within_element($element) ) {}
Function: Test if we are within a particular element
          This is different than 'in' because within can be tested
          for a whole block.
Returns : boolean
Args    : string element name

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🔥 in_element

Title   : in_element
Usage   : if( $eventgenerator->in_element($element) ) {}
Function: Test if we are in a particular element
          This is different than 'in' because within can be tested
          for a whole block.
Returns : boolean
Args    : string element name

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🌟 start_document

Title   : start_document
Usage   : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args    : none

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🌟 end_document

Title   : end_document
Usage   : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args    : none

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🍓 wise

Title   : wise
Usage   : $obj->wise($newval)
Function: Get/Set the Wise object parser
Returns : value of wise (a scalar)
Args    : on set, new value (a scalar or undef, optional)

get it, set it, iconic behavior ✨

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🍓 wisetype

Title   : wisetype
Usage   : $obj->wisetype($newval)
Function: Wise program type
Returns : value of wisetype (a scalar)
Args    : on set, new value (a scalar or undef, optional)

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and that's the whole page, bestie!! 🎀💜

cute lil sign-off: this was generated by perl v5.32.1, dated 2021-08-15, and it belongs to the fine folks at Bio::S...O::wise(3pm) 💖✨