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

🌸 NAME 🌸

Bio::Tools::Run::EMBOSSacd — the class that holds all the EMBOSS application qualifiers, aka the lil' keeper of every possible command-line argument an EMBOSS program could ever want. 💖

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✨ SYNOPSIS ✨

okay bestie, watch closely, this is the whole vibe:

# Get an EMBOSS factory
use Bio::Factory::EMBOSS;
$f = Bio::Factory::EMBOSS -> new();
# Get an EMBOSS application  object from the factory
$water = $f->program('water') || die "Program not found!\n";

# Here is an example of running the application - water can
# compare 1 sequence against 1 or more sequences using Smith-Waterman.
# Pass a Sequence object and a reference to an array of objects.

my $wateroutfile = 'out.water';
$water->run({-asequence => $seq_object,
             -bsequence => \@seq_objects,
             -gapopen   => '10.0',
             -gapextend => '0.5',
             -outfile   => $wateroutfile});

# Now you might want to get the alignment
use Bio::AlignIO;
my $alnin = Bio::AlignIO->new(-format => 'emboss',
                              -file   => $wateroutfile);

while ( my $aln = $alnin->next_aln ) {
    # process the alignment -- these will be Bio::SimpleAlign objects
}

it's giving factory pattern and honestly? we love that for us. 🦋

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🎀 DESCRIPTION 🎀

So basically the EMBOSSacd object is the main character that represents all the possible command line arguments you can hand to an EMBOSS application. every single one. no cap. 💅

Do not create this object directly. 🙈 It gets created and attached to its corresponding Bio::Tools::Run::EMBOSSApplication for you — but only if you set this:

$application->verbose > 0

Then to go get it, you call:

$application->acd

and boom, you've retrieved the Bio::Tools::Run::EMBOSSApplication::EMBOSSacd object. 🫶

Also go peek at Bio::Tools::Run::EMBOSSApplication and Bio::Factory::EMBOSS — they're the supporting cast, iykyk.

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💌 FEEDBACK 💌

🌈 Mailing Lists 🌈

User feedback is literally an integral part of the evolution of this and other Bioperl modules — like, we need it. Send your comments and suggestions preferably to the Bioperl mailing lists, your participation is much appreciated. ✨

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. Why? Because so many experienced and responsive experts will be able look at the problem and quickly address it — the way that works is honestly iconic. 👑

If at all possible, please include a thorough description of the problem with code and data examples. fr fr, the more detail the better. 💜

🦋 Reporting Bugs 🦋

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

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👑 AUTHOR - Heikki Lehvaslaiho 👑

Email: heikki-at-bioperl-dot-org

Address:

EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom

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🍓 APPENDIX 🍓

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (you know, the little secret ones 👀).

🧚 new

• Title: new
• Usage: $emboss_prog->acd($prog_name);
• Function: Constructor for the class. Calls EMBOSS program acdc, converts the HTML output into XML and uses XML::Twig XML parser to write out a hash of qualifiers which is then blessed. 💖
• Throws: without program name
• Returns: new object
• Args: EMBOSS program name

🧚 name

• Title: name
• Usage: $embossacd->name
• Function: sets/gets the name of the EMBOSS program. Setting is done by the EMBOSSApplication object, you should only get it. 🙅‍♀️
• Throws:
• Returns: name string
• Args: None

🧚 print

• Title: print
• Usage: $embossacd->print; $embossacd->print('-word');
• Function: Print out the qualifiers. Uses Data::Dumper to print the qualifiers into STDOUT. A valid qualifier name given as an argment limits the output.
• Throws:
• Returns: print string
• Args: optional qualifier name

🧚 mandatory

• Title: mandatory
• Usage: $acd->mandatory
• Function: gets a mandatory subset of qualifiers
• Throws:
• Returns: Bio::Tools::Run::EMBOSSacd object
• Args: none

💅 Qualifier queries 💅

These methods can be used test qualifier names and read values.

🧚 qualifier

• Title: qualifier
• Usage: $acd->qualifier($string)
• Function: tests for the existence of the qualifier
• Throws:
• Returns: boolean
• Args: string, name of the qualifier

🧚 category

• Title: category
• Usage: $acd->category($qual_name)
• Function: Return the category of the qualifier
• Throws:
• Returns: 'mandatory' or 'optional' or 'advanced' or 'associated' or 'general'
• Args: string, name of the qualifier

🧚 values

• Title: values
• Usage: $acd->values($qual_name)
• Function: Return the possible values for the qualifier
• Throws:
• Returns: string
• Args: string, name of the qualifier

🧚 descr

• Title: descr
• Usage: $acd->descr($qual_name)
• Function: Return the description of the qualifier
• Throws:
• Returns: boolean
• Args: string, name of the qualifier

🧚 unnamed

• Title: unnamed
• Usage: $acd->unnamed($qual_name)
• Function: Find if the qualifier can be left unnamed
• Throws:
• Returns: 0 if needs to be named, order number otherwise
• Args: string, name of the qualifier

🧚 default

• Title: default
• Usage: $acd->default($qual_name)
• Function: Return the default value for the qualifier
• Throws:
• Returns: scalar
• Args: string, name of the qualifier

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and that's the whole page bestie, we ate and left no crumbs 🍽️✨

perl v5.36.0, dated 2023-01-22, from the User Contributed Perl Documentation — mwah, thanks for reading, ily, go run some EMBOSS 💖🦋💅