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Bio::Tools::Run::AlignUser:Contributed)Bio::Tools::Run::Alignment::MSAProbs(3)

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

perl v5.32.1			  2021-Bio::Tools::Run::Alignment::MSAProbs(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jessen Bredeson | CONTRIBUTIONS | APPENDIX | Bio::Tools::Run::WrapperBase methods | Private Methods

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