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

🦋 Bio::T...::Proda(3pm) — aka Bio::Tools::Run::Alignment::Proda 💖

okay bestie, welcome to the manual page for Bio::T...::Proda(3pm) (yes that's the page name, and the actual module is the whole long thing, we'll get there). it's part of the User Contributed Perl Documentation, and it's lowkey iconic. let's go 💅

---

✨ NAME ✨

Bio::Tools::Run::Alignment::Proda — an object for the calculation of sets of multiple sequence alignments from a set of unaligned sequences or alignments, using the Proda program. that's the whole vibe. 🧬

---

🌸 SYNOPSIS 🌸

# Build a Proda alignment factory
$factory = Bio::Tools::Run::Alignment::Proda->new(@params);

# Pass the factory a list of sequences to be aligned.
$inputfilename = 't/cysprot.fa';
# @alns is an array of SimpleAlign objects.
@alns = $factory->align($inputfilename);

# or where @seq_array is an array of Bio::Seq objects
$seq_array_ref = \@seq_array;
@alns = $factory->align($seq_array_ref);

# Or one can pass the factory a pair of (sub)alignments
#to be aligned against each other, e.g.:

#There are various additional options and input formats available.
#See the DESCRIPTION section that follows for additional details.

$factory = Bio::Tools::Run::Alignment::Proda->new();
@alns = $factory->align($seq_array_ref);

---

💜 DESCRIPTION 💜

you can get it and see info about it at this URL: http://proda.stanford.edu ✨

so here's the tea: this program returns one or more local alignments for the different repeated or rearranged regions in your sequences. and if a sequence has more than one of those patterns in it? bestie, it's gonna show up more than once in the alignment. no cap. 🙈

the difference shows up in the id — it'll carry the start and end, like myseqid(123-456) and myseqid(567-890), instead of just plain myseqid like in the original input file. and this is true for all the output ids, even if they only show up once. periodt. 👑

🎀 Helping the module find your executable 🎀

you're gonna need to let Proda find the proda program. there are (at least) three ways to do this:

1. Make sure the proda executable is in your path (i.e.
   'which proda' returns a valid program
2. define an environmental variable PRODADIR which points to a
   directory containing the 'proda' app:
In bash
     export PRODADIR=/home/progs/proda   or
In csh/tcsh
     setenv PRODADIR /home/progs/proda

3. include a definition of an environmental variable PRODADIR
   in every script that will
  BEGIN {$ENV{PRODADIR} = '/home/progs/proda'; }
  use Bio::Tools::Run::Alignment::Proda;

---

🫶 FEEDBACK 🫶

🌈 Mailing Lists 🌈

user feedback is an integral part of the evolution of this and other Bioperl modules. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, fr fr. 💖

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. so many experienced and responsive experts 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. the more context the better, bestie. 🙏

💀 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:

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

---

👑 AUTHOR - Albert Vilella 👑

Email avilella-at-gmail-dot-com

---

⭐ APPENDIX ⭐

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — that's the secret handshake, iykyk. 🤫

🧚 program_name

• Title: program_name
• Usage: $factory->program_name()
• Function: holds the program name
• Returns: string
• Args: None

🧚 program_dir

• Title: program_dir
• Usage: $factory->program_dir(@params)
• Function: returns the program directory, obtained from ENV variable.
• Returns: string
• Args:

🧚 new

• Title: new
• Usage: my $proda = Bio::Tools::Run::Alignment::Proda->new();
• Function: Constructor
• Returns: Bio::Tools::Run::Alignment::Proda
• Args: -outfile_name => $outname

🧚 error_string

• Title: error_string
• Usage: $obj->error_string($newval)
• Function: Where the output from the last analysus run is stored.
• Returns: value of error_string
• Args: newvalue (optional)

🧚 version

• Title: version
• Usage: exit if $prog->version() < 1.8
• Function: Determine the version number of the program
• Example:
• Returns: float or undef
• Args: none

🧚 run

• Title: run
• Usage: my $output = $application->run(\@seqs);
• Function: Generic run of an application
• Returns: Bio::SimpleAlign object
• Args: Arrayref of Bio::PrimarySeqI objects or a filename to run on

🧚 align

• Title: align
• Usage:

$inputfilename = 't/data/cysprot.fa';
$aln = $factory->align($inputfilename);

or

$seq_array_ref = \@seq_array;
# @seq_array is array of Seq objs
$aln = $factory->align($seq_array_ref);

• Function: Perform a multiple sequence alignment
• Returns: Reference to a SimpleAlign object containing the sequence alignment.
• Args: Name of a file containing a set of unaligned fasta sequences or else an array of references to Bio::Seq objects.

it throws an exception if the argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. if the argument is a string, it throws an exception if the file corresponding to the string name can not be found. and if the argument is a Bio::Seq array, it throws an exception if there are less than two sequence objects in the array. two minimum, bestie, it's a whole alignment. 😭

🧚 _run

• Title: _run
• Usage: Internal function, not to be called directly
• Function: makes actual system call to proda program
• Example:
• Returns: nothing; proda output is written to a temporary file OR specified output file
• Args: Name of a file containing a set of unaligned fasta sequences and hash of parameters to be passed to proda

🧚 _setinput

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: Create input file for proda program
• Example:
• Returns: name of file containing proda data input AND
• Args: Arrayref of Seqs or input file name

🧚 _setparams

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: Create parameter inputs for proda program
• Example:
• Returns: parameter string to be passed to proda during align or profile_align
• Args: name of calling object

🧚 aformat

• Title: aformat
• Usage: my $alignmentformat = $self->aformat();
• Function: Get/Set alignment format
• Returns: string
• Args: string

---

💖 Bio::Tools::Run::BaseWrapper methods 💖

🦋 no_param_checks

• Title: no_param_checks
• Usage: $obj->no_param_checks($newval)
• Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values
• Returns: value of no_param_checks
• Args: newvalue (optional)

🦋 save_tempfiles

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

🦋 outfile_name

• Title: outfile_name
• Usage: my $outfile = $proda->outfile_name();
• Function: Get/Set the name of the output file for this run (if you wanted to do something special)
• Returns: string
• Args: [optional] string to set value to

🦋 tempdir

• Title: tempdir
• Usage: my $tmpdir = $self->tempdir();
• Function: Retrieve a temporary directory name (which is created)
• Returns: string which is the name of the temporary directory
• Args: none

🦋 cleanup

• Title: cleanup
• Usage: $proda->cleanup();
• Function: Will cleanup the tempdir directory
• Returns: none
• Args: none

🦋 io

• Title: io
• Usage: $obj->io($newval)
• Function: Gets a L<Bio::Root::IO> object
• Returns: L<Bio::Root::IO>
• Args: none

---

and that's the whole page, bestie!! 🎀 this lil' gem is from perl v5.36.0, dated 2023-01-22, and it lives under the name Bio::T...::Proda(3pm) — go forth and align some sequences, you absolute main character. slay. 💅✨🦋