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

💖 Bio::S...O::psl 💖

okay bestie, so this is a page from the User Contributed Perl Documentation, and the module is Bio::S...O::psl (that's the manpage name, she's shy, she abbreviates) 🦋

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✨ NAME ✨

Bio::SearchIO::psl — a parser for PSL output (UCSC) 🌸

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🎀 SYNOPSIS 🎀

no cap, this is literally all you need:

use Bio::SearchIO;
my $parser = Bio::SearchIO->new(-file   => 'file.psl',
                               -format => 'psl');
while( my $result = $parser->next_result ) {
}

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💅 DESCRIPTION 💅

so this is a SearchIO driver for the PSL format. PSL format is documented right here, bestie, go read it:

http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL

By default it assumes your PSL output came from BLAT 🐦 but you can totally override that by passing -program_name => 'BLASTZ' when you init the SearchIO object. it's giving customizable, it's giving flexibility, we love that for you ✨

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🫶 FEEDBACK 🫶

🌈 Mailing Lists

user feedback is like, an integral part of the evolution of this and other Bioperl modules, fr fr. 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

🌸 Support

okay so pls direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

...rather than to the module maintainer directly. there are so many experienced and responsive experts who will be able look at the problem and quickly address it 👑 and if you can, pls include a thorough description of the problem with code and data examples, like, at all possible. thoroughness is the vibe check.

🐛 Reporting Bugs

report bugs 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-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 _ (iykyk, the underscore is the secret handshake) 🤫

new

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

builds a brand new Bio::SearchIO::psl object, and hands you back an instance of Bio::SearchIO::psl. the Args line is empty, she takes no arguments here, she's low maintenance 💅

next_result

Title   : next_result
Usage   : my $result = $parser->next_result
Function: Parse the next result from the data stream
Returns : L<Bio::Search::Result::ResultI> or undef if no more results
Args    : none

parses the next result off the data stream 🌊 returns a Bio::Search::Result::ResultI object, or undef when there's literally nothing left. no args, none, nada.

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' ✨

end_element

Title   : end_element
Usage   : $eventgenerator->end_element
Function: Handles an end element event
Returns : return value from the associated end_$type event handler
Args    : hashref with at least 2 keys 'Data' and 'Name'

handles an end element event. what does it return? the return value from the associated end_$type event handler, periodt. args: hashref with at least 2 keys, 'Data' and 'Name' 💖

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'

the convenience method that calls start_element, characters, then end_element — she's the main character who does all three 😌 returns none. args: 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. returns none. takes a string 🦋

_mode

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

internal one, note the underscore 🙈 returns the value of _mode. the Function and Example lines are empty — she's mysterious like that. args: newvalue, optional.

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 if we're within a particular element. and heads up — this is different than 'in' because within can be tested for a whole block. returns a boolean. takes a string element name 💜

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 if we're in a particular element. same note as above: this is different than 'in' because within can be tested for a whole block. returns a boolean. takes a string element name 🌸

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 no args. simple, clean, iconic ✨

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. returns a Bio::Search::Result::ResultI object. no args 👑

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 so far. returns an integer. no args, she just knows 🔢

program_name

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

get/set the program name. returns the value of program_name, a scalar. on set, the new value (a scalar or undef, optional) 🎀

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and that's the whole page bestie, you ate it 💅✨

perl v5.32.1 · 2021-08-15 — that's the version and date, mwah, go forth and parse 🦋💖