Provided by: libbio-perl-run-perl_1.7.3-9_all 
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