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

💖 Bio::Tools::Run::Alignment::Probalign — the Perl doc page, but make it make sense 💖

okay bestie, this is a User Contributed Perl Documentation page for Bio::Tools::Run::Alignment::Probalign, and it is literally the whole vibe of "let me run Probalign for you from Perl without you having to touch a shell." Sit down, grab a strawberry 🍓, and let's go.

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✨ NAME ✨

Bio::Tools::Run::Alignment::Probalign — an Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program. 🧬

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🎀 SYNOPSIS 🎀

Build a muscle alignment factory, bestie:

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

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

# or where @seq_array is an array of Bio::Seq objects
$seq_array_ref = \@seq_array;
$aln = $factory->align($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::Probalign->new();
$factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
$aln = $factory->align($seq_array_ref);

that's it. that's the whole entry point. you feed it sequences (or a filename, or a ref to an array of Bio::Seq objects) and it hands you back an alignment. iconic behavior honestly. 👑

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🌸 DESCRIPTION 🌸

Probalign: multiple sequence alignment using partition function posterior probabilities.

Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. You can get it and see information about it at this URL:

http://www.cs.njit.edu/usman/probalign

no cap, go look at it, the posteriors are the whole point. ✨

🦋 Helping the module find your executable

You will need to enable Probalign to find the probalign program. This can be done in (at least) three ways:

1. Make sure the probalign executable is in your path (i.e. which probalign returns a valid program
2. define an environmental variable PROBALIGNDIR which points to a directory containing the probalign app: In bash

export PROBALIGNDIR=/home/progs/probalign   or

In csh/tcsh

setenv PROBALIGNDIR /home/progs/probalign

3. include a definition of an environmental variable PROBALIGNDIR in every script that will

BEGIN {$ENV{PROBALIGNDIR} = '/home/progs/probalign'; }
use Bio::Tools::Run::Alignment::Probalign;

💀 bestie if which probalign comes back empty, nothing downstream is gonna work. pick a lane, any of the three lanes.

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🫶 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. 💜

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. Many 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.

fr fr, include the code and the data. the experts are responsive but they are not psychic. 🙈

🐛 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 - Albert Vilella 👑

Email avilella-at-gmail-dot-com

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⭐ APPENDIX ⭐

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

🧚 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 $probalign = Bio::Tools::Run::Alignment::Probalign->new();
Function: Constructor
Returns : Bio::Tools::Run::Alignment::Probalign
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.

Throws an exception if argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. If argument is string, throws exception if file corresponding to string name can not be found. If argument is Bio::Seq array, throws exception if less than two sequence objects are in array.

⚠️ so like, don't hand it a hash, don't hand it one lonely sequence. two sequences minimum or it's throwing hands (an exception). 💅

🧚 _run

Title   :  _run
Usage   :  Internal function, not to be called directly
Function:  makes actual system call to probalign program
Example :
Returns : nothing; probalign 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 probalign

🧚 _setinput

Title   :  _setinput
Usage   :  Internal function, not to be called directly
Function:  Create input file for probalign program
Example :
Returns : name of file containing probalign 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 probalign program
Example :
Returns : parameter string to be passed to probalign
          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

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💅 Bio::Tools::Run::BaseWrapper methods 💅

these ones you inherited, bestie. still yours to use.

🌟 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 = $probalign->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   : $probalign->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

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🎀 and that's the whole page, bestie. internal methods start with _, so if you're calling _run, _setinput or _setparams directly, that's on you. 😭

okay that's a wrap 💖 this was Bio::T...obalign(3pm) from perl v5.36.0, dated 2023-01-22, and you read the whole thing. main character energy, genuinely. slay. periodt. 👑✨🦋