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

📦
version 1.7.3 · 3 versions
, in debian bookworm, ubuntu noble

💖 NAME 💖

Bio::Tools::Run::Alignment::MSAProbs — bestie, this is the object that does the whole multiple sequence alignment (MSA) thing: you hand it a set of unaligned sequences, it hands you back a beautiful alignment using the MSAProbs program. That's the gig. (This page lives under the manual name Bio::T...AProbs(3pm), iykyk 💅)

✨ SYNOPSIS ✨

# Build a msaprobs alignment factory
$factory = Bio::Tools::Run::Alignment::MSAProbs->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);

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

🌸 DESCRIPTION 🌸

MSAProbs is Liu, Schmidt, and Maskell's (2010) alignment program, and it eats HMM and partition function posterior probabilities for breakfast. For a way more in-depth description, go read the original publication, no cap:

Liu, Y., Schmidt, B., and Maskell, D. L. (2010) MSAProbs: multiple
sequence alignment based on pair hidden Markov models and partition
function posterior probabilities. I<Bioinformatics> 26(16): 1958-1964
doi:10.1093/bioinformatics/btq338

-OR-

http://bioinformatics.oxfordjournals.org/content/26/16/1958.abstract

You can download the source code from http://sourceforge.net/projects/msaprobs/ 🫶

Heads up, bestie: it is recommended you use at least version 0.9 — behaviour with earlier versions is questionable, and not in a cute way. 💀

🧚 Helping the module find your executable

You will need to help MSAProbs find the 'msaprobs' executable. There are (at least) three ways to do this, and honestly pick whichever one vibes with you:

  1. Make sure the msaprobs executable is in your path (i.e. 'which msaprobs' returns a valid program)
  2. define an environmental variable MSAPROBSDIR which points to a directory containing the 'msaprobs' app:

In bash

export MSAPROBSDIR=/home/progs/msaprobs   or

In csh/tcsh

setenv MSAPROBSDIR /home/progs/msaprobs
  1. include a definition of an environmental variable MSAPROBSDIR in every script that will
BEGIN {$ENV{MSAPROBSDIR} = '/home/progs/msaprobs'; }
use Bio::Tools::Run::Alignment::MSAProbs;

💌 FEEDBACK 💌

Mailing Lists

User feedback is literally 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. There are so many experienced and responsive experts on there who will be able to 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 to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

👑 AUTHOR - Jessen Bredeson 👑

Email jessenbredeson@berkeley.edu

🌈 CONTRIBUTIONS 🌈

This MSAProbs module was adapted from the Bio::Tools::Run::Alignment::Muscle module, written by Jason Stajich, and almost all of the credit should be given to him. King behaviour. 👑

Email jason-at-bioperl-dot-org

🎀 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 :

🔥 version

  • Title : version
  • Usage : exit if $prog->version() < 0.9.4
  • Function: Determine the version number of the program
  • Example :
  • Returns : float or undef
  • Args : none

🔥 new

  • Title : new
  • Usage : my $msaprobs = Bio::Tools::Run::Alignment::MSAProbs->new();
  • Function: Constructor
  • Returns : Bio::Tools::Run::Alignment::MSAProbs
  • Args : -outfile => $outname

🔥 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.
Drama alert: 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. If the argument is a Bio::Seq array, it throws an exception if there are less than two sequence objects in the array.

🔥 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)

🔥 infile

  • Title : infile
  • Usage : $prog->infile($filename)
  • Function: get/set the fasta (and only a fasta) file to run on or the array reference containing the Bio::SeqI objects
  • Returns : name of input sequence file or object array ref
  • Args : name of input sequence file or object array ref

🔥 outfile

  • Title : outfile
  • Usage : $prog->outfile($filename)
  • Function: get/set the file to save output to
  • Returns : outfile name if set
  • Args : newvalue (optional)

🔥 annot_file

  • Title : annot_file
  • Usage : $prog->annot_file($filename)
  • Function: get/set the file name to write the MSA annotation to
  • Returns : filename or undef
  • Args : filename (optional)

🔥 num_threads

  • Title : num_threads
  • Usage : $prog->num_threads($cores)
  • Function: get/set number of cores on your machine
  • Returns : integer
  • Args : integer (optional; executable auto-detects)

🔥 consistency

  • Title : consistency
  • Usage : $prog->consistency($passes)
  • Function: get/set the number of consistency transformation passes
  • Returns : integer
  • Args : integer 0..5, [default 2] (optional)

🔥 iterations

  • Title : iterations
  • Usage : $prog->iterations($passes)
  • Function: get/set the number of iterative-refinement passes
  • Returns : integer
  • Args : integer 0..1000, [default 10] (optional)

🔥 alignment_order

  • Title : alignment_order
  • Usage : $prog->alignment_order($bool)
  • Function: specify whether or not to output aligned sequences in alignment order, not input order
  • Returns : boolean
  • Args : boolean [default: off] (optional)

🔥 clustalw

  • Title : clustalw
  • Usage : $prog->clustalw($bool)
  • Function: write output in clustalw format; makes no sense unless outfile() is also specified
  • Returns : boolean
  • Args : boolean [default: off] (optional)

💜 Bio::Tools::Run::WrapperBase 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 = $msaprobs->outfile_name();
  • Function: Get the name of the output file from a run (if you wanted to do something special)
  • Returns : string
  • Args : none

🦋 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 : $msaprobs->cleanup();
  • Function: Will cleanup the tempdir directory
  • Returns : none
  • Args : none

🦋 io

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

🙈 Private Methods 🙈

🍓 _run

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

🍓 _setinput

  • Title : _setinput
  • Usage : Internal function, not to be called directly
  • Function: Create input file for msaprobs program
  • Example :
  • Returns : name of file containing msaprobs 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 msaprobs program
  • Example :
  • Returns : parameter string to be passed to msaprobs during align
  • Args : name of calling object

🍓 aformat

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

And that's the whole page, bestie — written for perl v5.36.0 and dated 2023-01-22, which is honestly giving vintage in the best way. Go align something iconic. 💅✨🦋

📦 where this page comes from