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

NAME
       Bio::Tools::Run::Alignment::Probcons - Object for the calculation of an
       iterative multiple sequence alignment from a set	of unaligned sequences
       or alignments using the Probcons	program

SYNOPSIS
	 # Build a muscle alignment factory
	 $factory = Bio::Tools::Run::Alignment::Probcons->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);

	 # Or one can pass the factory a pair of (sub)alignments
	 #to be	aligned	against	each other, e.g.:

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

	 #To run probcons with training, try something like:

	 #First	round to generate train.params
	 $factory = Bio::Tools::Run::Alignment::Probcons->new
	     (
	      'iterative-refinement'  => '1000',
	      'consistency'   => '5',
	      'pre-training' =>	'20',
	      'emissions' => '',
	      'verbose'	=> '',
	      'train'	=> "$dir/$subdir/$outdir/train.params",
	     );
	 $factory->outfile_name("$dir/$subdir/$outdir/train.params");

	 #Second round to use train.params to get a high qual alignment

	 $seq_array_ref	= \@seq_array;
	 $aln =	$factory->align($seq_array_ref);
	 $aln =	'';
	 $factory = '';

	 $factory = Bio::Tools::Run::Alignment::Probcons->new
	     (
	      'iterative-refinement'  => '1000',
	      'consistency'   => '5',
	      'pre-training' =>	'20',
	      'verbose'	=> '',
	      'paramfile'   => "$dir/$subdir/$outdir/train.params",
	     );
	 $factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
	 $aln =	$factory->align($seq_array_ref);

DESCRIPTION
       Probcons	is a Probabilistic Consistency-based Multiple Alignment	of
       Amino Acid Sequences. You can get it and	see information	about it at
       this URL	http://probcons.stanford.edu/

   Helping the module find your	executable
       You will	need to	enable Probcons	to find	the probcons program. This can
       be done in (at least) three ways:

	 1. Make sure the probcons executable is in your path (i.e.
	    'which probcons' returns a valid program
	 2. define an environmental variable PROBCONSDIR which points to a
	    directory containing the 'probcons'	app:
	  In bash
	       export PROBCONSDIR=/home/progs/probcons	 or
	  In csh/tcsh
	       setenv PROBCONSDIR /home/progs/probcons

	 3. include a definition of an environmental variable PROBCONSDIR
	     in	every script that will
	    BEGIN {$ENV{PROBCONSDIR} = '/home/progs/probcons'; }
	    use	Bio::Tools::Run::Alignment::Probcons;

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://redmine.open-bio.org/projects/bioperl/

AUTHOR -  Jason	Stajich
       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	:

   new
	Title	: new
	Usage	: my $probcons = Bio::Tools::Run::Alignment::Probcons->new();
	Function: Constructor
	Returns	: Bio::Tools::Run::Alignment::Probcons
	Args	: -outfile_name	=> $outname

   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)

   version
	Title	: version
	Usage	: exit if $prog->version() < 1.8
	Function: Determine the	version	number of the program
	Example	:
	Returns	: float	or undef
	Args	: none

   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.

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

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

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

Bio::Tools::Run::BaseWrapper 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 =	$probcons->outfile_name();
	Function: Get/Set the name of the output file for this run
		  (if you wanted to do something special)
	Returns	: string
	Args	: [optional] string to set value to

   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	: $probcons->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

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX | Bio::Tools::Run::BaseWrapper methods

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