Bio::F...EMBOSS(3pm)

🎀 Bio::F...EMBOSS 🎀

okay bestie, listen. this is Bio::F...EMBOSS, a page from the User Contributed Perl Documentation collection, and it's literally the manual for the EMBOSS application factory class. it's giving "build me a Perl object that knows how to run EMBOSS programs" energy and honestly? we're obsessed. 💅

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✨ NAME ✨

Bio::Factory::EMBOSS — the EMBOSS application factory class. it makes EMBOSS app objects, that's the whole job, she's a queen. 👑

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🌸 SYNOPSIS 🌸

okay so here's the vibe in code, no cap:

# 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
}

so first you grab a factory, then you pull a program object out of it. water is doing the Smith-Waterman thing where it compares 1 sequence against 1 or more sequences — you hand it a Sequence object and a reference to an array of objects. then you can slurp the alignment back out with Bio::AlignIO and the emboss format, and every $aln you get is a Bio::SimpleAlign object. ate. 🔥

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💜 DESCRIPTION 💜

the EMBOSS factory class wraps up access to EMBOSS programs. a factory object can only ever create applications it already knows about — no mystery programs, we don't do that here. 🙈

if you wanna check command line options before shipping them off to the program, just set $prog->verbose to a positive integer. that value gets passed along to the program objects, and the ADC description of the available command line options gets parsed and compared against what you put in. vibe check, but for flags. ⭐

also see Bio::Tools::Run::EMBOSSApplication and Bio::Tools::Run::EMBOSSacd. iykyk. 🦋

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🫶 FEEDBACK 🫶

🌈 Mailing Lists 🌈

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, the glow-up is a group project. 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. there are many experienced and responsive experts who will be able to look at the problem and quickly address it. and please include a thorough description of the problem with code and data examples if at all possible — receipts, bestie, we need the receipts. 📎

💀 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:

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

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👑 AUTHOR - Heikki Lehvaslaiho 👑

Email: heikki-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 _ — that underscore is the "do not perceive me" marker, respect it. 💅

⭐ location ⭐

• Title : location
• Usage : $embossfactory->location
• Function : get/set the location of EMBOSS programs. Valid values are 'local' and 'novella'.
• Returns : string, defaults to 'local'
• Args : string

⭐ program ⭐

• Title : program
• Usage : $embossfactory->program('program_name')
• Function : Creates a representation of a single EMBOSS program and issues a warning if the program was not found.
• Returns : Bio::Tools::Run::EMBOSSApplication object or undef
• Args : string, program name

⭐ version ⭐

• Title : $self->version
• Usage : $embossfactory->version()
• Function : gets the version of EMBOSS programs
• Throws : if EMBOSS suite is not accessible
• Returns : version value
• Args : None

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💖 Programs 💖

these methods allow the programmer to query the EMBOSS suite and find out which program names can be used and what arguments can be used. it's giving detective work, but make it bioinformatics. 🔍

🌟 program_info 🌟

• Title : program_info
• Usage : $embossfactory->program_info('emma')
• Function : Finds out if the program is available.
• Returns : definition string of the program, undef if program name not known
• Args : string, prgramname

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🙈 Internal methods 🙈

do not call these methods directly. i said what i said. 😭

🍓 _program_list 🍓

• Title : _program_list
• Usage : $embossfactory->_program_list()
• Function : Finds out what programs are available. Writes the names into an internal hash.
• Returns : true if successful
• Args : None

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and that's the whole page, bestie!! this one's perl v5.36.0, dated 2023-01-22, and it lives under the name Bio::F...EMBOSS(3pm) in the User Contributed Perl Documentation. go forth and run some EMBOSS programs, you've got this. 💖✨🎀