NAME

Bio::Tools::Run::Alignment::MSAProbs - Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program

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 using HMM and partition function posterior probabilities. For more a more in-depth description see the original publication:

    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/

It is recommended you use at least version 0.9; behaviour with earlier versions is questionable.

Helping the module find your executable

You will need to help MSAProbs to find the 'msaprobs' executable. This can be done in (at least) three ways:

  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
  3. 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 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.

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://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.

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.
 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.

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 L<Bio::Root::IO> object
 Returns : L<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