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

💖 NAME

Bio::Tools::Run::EMBOSSApplication — bestie, it's the class for EMBOSS Applications ✨

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✨ SYNOPSIS

# 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
}

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🦋 DESCRIPTION

Okay so EMBOSSApplication can literally be any EMBOSS program, no cap. It gets made by a Bio::Factory::EMBOSS object. 👑

If you wanna vibe check your command line options before you yeet them at the program, set $prog->verbose to a positive integer. Then the ADC description of the available command line options gets parsed in and compared to your input. So cute, so responsible. 💅

Also go look at Bio::Factory::EMBOSS and Bio::Tools::Run::EMBOSSacd — they're the friends of this module, iykyk. 🫶

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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 lists, your participation is so 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. Lots of 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. 🙏

Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can 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

CONTRIBUTORS

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 _ (the little secret ones, you know how it is 💀).

run

• Title: run
• Usage: $embossapplication->run($attribute_hash)
• Function: Runs the EMBOSS program. 🏃♀️
• Returns: string or creates files for now; will return objects! (future plans, bestie)
• Args: hash of input to the program

acd

• Title: acd
• Usage: $embossprogram->acd
• Function: finds out all the possible qualifiers for this EMBOSS application. They can be used to debug the options given. 🔍
• Throws:
• Returns: boolean
• Args:

name

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

descr

• Title: descr
• Usage: $embossprogram->descr
• Function: sets/gets the descr of the EMBOSS program. Setting is done by the EMBOSSFactory object, you should only get it.
• Throws:
• Returns: description string
• Args: None

group

• Title: group
• Usage: $embossprogram->group
• Function: sets/gets the group of the EMBOSS program. Setting is done by the EMBOSSFactory object, you should only get it.

If the application is assigned into a subgroup use l<subgroup> to get it.

• Throws:
• Returns: string, group name
• Args: group string

subgroup

• Title: subgroup
• Usage: $embossprogram->subgroup
• Function: sets/gets the subgroup of the EMBOSS program. Setting is done by the EMBOSSFactory object, you should only get it.
• Throws:
• Returns: string, subgroup name; undef if not defined
• Args: None

program_dir

• Title: program_dir
• Usage:
• Function: Required by WrapperBase
• Throws:
• Returns: Name of directory with EMBOSS programs
• Args:

program_path

• Title: program_path
• Usage:
• Function: Required by WrapperBase
• Throws:
• Returns: Full path of program
• Args:

executable

• Title: executable
• Usage:
• Function: Required by WrapperBase
• Throws:
• Returns: Name of program
• Args:

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That's the whole page, bestie, you ate it. 🍓 This one came from the User Contributed Perl Documentation, running perl v5.36.0, dated 2023-01-22 — go off, icon. 💅✨