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

💖 Bio::S...O::axt 💖

okay so bestie, welcome to the manual page for Bio::S...O::axt — a little parser gem from the User Contributed Perl Documentation collection. it's a Perl module, it lives in the 3pm section of your man pages, and it is so good at what it does. let's get into it 🫶

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✨ NAME ✨

Bio::SearchIO::axt — it's a parser for axt format reports. that's it, that's the whole job, and it does it flawlessly 💅

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🌸 SYNOPSIS 🌸

here's the vibe, the whole flow, the main character moment:

use Bio::SearchIO;
my $parser = Bio::SearchIO->new(-format => 'axt',
                               -file   => 't/data/report.blastz');
while( my $result = $parser->next_result ) {
  while( my $hit = $result->next_hit ) {
    while( my $hsp = $hit->next_hsp ) {
    }
  }
}

like… nested loops going result → hit → hsp and you just sit there like 💀 it's giving "I contain multitudes" and honestly? correct.

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🦋 DESCRIPTION 🦋

so this thing is a parser and an event-generator for AXT format reports. periodt.

BLASTZ reports (that's Schwartz et al,(2003) Genome Research, 13:103-107 — cite your sources babes 📚) are normally in LAV format, but bestie, they get post-processed into AXT format all the time. like, so many precomputed BLASTZ reports — the ones chilling in the UCSC Genome Browser? — are in AXT format. iconic behavior.

and here's the slay: this parser will also parse any AXT format produced from any lav report, and directly out of BLAT. versatile queen 👑

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💌 FEEDBACK 💌

💜 Mailing Lists 💜

user feedback is literally an integral part of the evolution of this and other Bioperl modules. no cap. so please, send your comments and suggestions to the Bioperl mailing list — your participation is much appreciated, we mean it 🥹

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

🫶 Support 🫶

okay so, usage questions and support issues? direct them to the mailing list:

bioperl-l@bioperl.org

not to the module maintainer directly. i know, i know, but trust the process — there are lots of experienced and responsive experts on there who will look at your problem and address it quickly. and please, for the love of everything, include a thorough description of the problem with code and data examples if at all possible. we're begging 🙏

🐛 Reporting Bugs 🐛

found a bug? report it to the Bioperl bug tracking system so we can 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 (yes, swap the -at- for an @, you got this 💖)

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📖 APPENDIX 📖

the rest of the documentation breaks down each of the object methods, one by one. heads up: internal methods are usually preceded with a _ — that underscore is like a little "staff only" velvet rope 🎀

🌟 new

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

builds a brand new Bio::SearchIO::axt object. newborn baby module. no args needed, it just exists ✨

🌟 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

hands you the next Result from a search as a Bio::Search::Result::ResultI object. no args, just vibes.

🌟 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'

handles a start element event. returns nothing, takes a hashref with at least 2 keys: 'Data' and 'Name'. that's the whole deal 🍓

🌟 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'

handles an end element event. returns none, takes a hashref with at least 2 keys: 'Data' and 'Name'.

ngl the Title line up there says start_element and honestly? we're keeping it exactly as it is, no cap. the original said it, so we say it 💀

🌟 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'

a convenience method (spelled Convience in the original, and we are not touching it) that calls start_element, characters, and end_element all in one go. a three-in-one combo meal 🍔 returns none, takes a hash ref with the keys 'Name' and 'Data'.

🌟 characters

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

sends a character event (the original says "Send a character events" — plural energy, we respect it). returns none, takes a string. simple as 🌈

🌟 _mode

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

internal method (see that _? velvet rope 💅). returns the value of _mode, takes an optional newvalue as the arg. the Function and Example lines are empty in the original and we are keeping them empty, because honesty is beautiful.

🌟 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

tests whether we're within a particular element. returns a boolean, takes a string element name.

and bestie, listen: this is different than 'in' because within can be tested for a whole block. whole-block energy, not just a moment. okay? okay 🫶

🌟 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

tests whether we're in a particular element. returns a boolean, takes a string element name.

same note as above (the original repeats it, so we repeat it): it's different than 'in' because within can be tested for a whole block. yes the original's wording is a little loopy here. yes we're keeping it. we don't make the rules, we just slay them ✨

🌟 start_document

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

handles a start document event. returns none, takes none. minimalism. 🤍

🌟 end_document

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

handles an end document event and returns a Bio::Search::Result::ResultI object. no args. closing time, but make it ✨academic✨

🌟 result_count

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

returns the number of results we've processed, as an integer. no args. it's the "how many have we done" counter and honestly it's so satisfying to watch it go up 🔥

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🎀 a lil sign-off 🎀

this page is from perl v5.32.1, dated 2021-08-15, and it's part of the User Contributed Perl Documentation — so yeah, user contributed, meaning people just like us wrote it and put it here for us. obsessed with that fr fr 🦋

go parse something gorgeous. you got this. mwah 💖💅✨