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

💖 Bio::SearchIO::waba — bestie edition 💖

okay so this is Bio::SearchIO::waba, a SearchIO parser for the Jim Kent WABA program alignment output. it lives in the Bio::SearchIO::waba manpage (perl v5.32.1, 2021-08-15). come sit with me, this one's short but she's got LORE. 🦋

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✨ NAME ✨

Bio::SearchIO::waba — SearchIO parser for Jim Kent WABA program alignment output

like. that's the whole thing. she's a parser. she parses WABA. no cap. 💅

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✨ SYNOPSIS ✨

bestie hear me LOUD: do not use this object directly, rather through Bio::SearchIO. fr fr. that's not a suggestion that's the whole vibe.

# do not use this object directly, rather through Bio::SearchIO

use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'waba',
                            -file   => 'output.wab');
while( my $result = $in->next_result ) {
    while( my $hit = $result->next_hit ) {
        while( my $hsp = $result->next_hsp ) {

        }
    }
}

look at those nested whiles. result → hit → hsp. it's giving russian nesting dolls but make it bioinformatics. the innermost block is empty because that's where you live, bestie. that's your main character moment. ✨

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✨ DESCRIPTION ✨

This parser will process the waba output (NOT the human readable format).

okay that "NOT" is in the original and it's in caps because they MEAN it. the human readable format? not it. don't even try. this parser wants the raw waba output and nothing else. she's picky. respect 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.

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

ngl the way the Bioperl community genuinely wants your feedback? that's community. that's iconic. your participation is much appreciated, and they said it, not me. 🫶

🌸 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.

bestie PLEASE. do not DM the maintainer. do not slide into their inbox. go to the mailing list. there are experienced and reponsive experts there who will look at your problem and quickly address it. (yes, "reponsive" is spelled like that in the original — we don't fix, we preserve. 🎀)

and when you post? include a thorough description of the problem, with code and data examples if at all possible. help them help you. that's the assignment. 💜

🌸 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

bug reports = keeping track of bugs AND their resolution. it's a whole system. it's organized. we love a process. 🐛✨

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✨ AUTHOR - Jason Stajich ✨

Email jason-at-bioperl.org

shoutout Jason. 👑 (also note: jason-at-bioperl.org — the "at" is written out like that, that's the anti-spam vibe, keep it exact.)

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✨ APPENDIX ✨

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

iykyk: if it starts with an underscore, it's internal. that's the tell. peek behind the curtain all you want, just know she's private. 🙈

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🌈 new 🌈

Title   : new
Usage   : my $obj = Bio::SearchIO::waba->new();
Function: Builds a new Bio::SearchIO::waba object
Returns : Bio::SearchIO::waba
Args    : see Bio::SearchIO

• Title — new
• Usage — my $obj = Bio::SearchIO::waba->new();
• Function — Builds a new Bio::SearchIO::waba object
• Returns — Bio::SearchIO::waba
• Args — see Bio::SearchIO

building a whole new object. fresh start. new era. ✨

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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

• 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

(notice the usage line names it $hit even though it's a result. we don't question. we copy verbatim. 💀)

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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'

• 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'

two keys minimum: 'Data' and 'Name'. that's the bare minimum. don't show up with one. 💅

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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'

• 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'

okay yes the Title says start_element for end_element. that's in the original. it's a lil typo and it's our typo now. keeping it. 😭

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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'

• 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'

she's a convenience method (spelled "Convience" in the original — we preserve, we don't correct) that does three things in one. start, characters, end. combo move. 🎀

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🌈 characters 🌈

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

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

one string in, character events out. (yes "a character events". plural energy. we keep.) 🍓

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🌈 _mode 🌈

Title   : _mode
Usage   : $obj->_mode($newval)
Function:
Example :
Returns : value of _mode
Args    : newvalue (optional)

• Title — _mode
• Usage — $obj->_mode($newval)
• Function — (blank in the original, so it stays blank here bestie)
• Example — (also blank, we don't invent)
• Returns — value of _mode
• Args — newvalue (optional)

the underscore! she's internal. and her Function is literally empty. mystery mode. enigmatic. we stan an unbothered queen who says nothing. 💅

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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

• 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

okay so the KEY tea here: this is different than 'in' because within can be tested for a whole block. whole block, bestie. that's the distinction. don't mix them up. 🔥

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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

• 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

same description text as within_element, copy-pasted right down to the wording. that's the original's choice, not mine, and I am not editing it. 🙈

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🌈 start_document 🌈

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

• Title — start_document
• Usage — $eventgenerator->start_document
• Function — Handles a start document event
• Returns — none
• Args — none

no args. no returns. just vibes and document-starting. ✨

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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

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

and she RETURNS something! unlike start_document who returns none. end_document understood the assignment. 👑

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🌈 result_count 🌈

Title   : result_count
Usage   : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args    : none

• Title — result_count
• Usage — my $count = $searchio->result_count
• Function — Returns the number of results we have processed
• Returns — integer
• Args — none

counting results. keeping score. math girlie. 🧮💖

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that's the whole page, bestie. every option, every arg, every blank Function field, every typo — preserved with love and a lil glitter on top. go parse some WABA. 🦋

perl v5.32.1 · 2021-08-15 · Bio::S...O::waba(3pm) — mwah, that's the sign-off, thanks for reading the docs with me 💅💖✨