/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Alignment::MSAProbs

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