pc-project(1) [debian man page]

PC-PROJECT(1)							  Probcons Manual						     PC-PROJECT(1)

NAME

       pc-project - Program to project multiple alignment to pairwise alignments.

SYNOPSIS

       pc-project [ALIGNMENT] [-nocompressgaps]

NOTE

       pc-project is named project in the original sources, but has been remamed to avoid collision with other program names.

SEE ALSO

       pc-makegnufile(1), pc-compare(1),from the probcons-extra package, and probcons(1) and probcons-RNA(1) from the probcons package.

REFERENCE

       Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence
       Alignment. Genome Research 15: 330-340.

AUTHORS

       Chuong Do <chuongdo@cs.stanford.edu>
	   Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science,
	   Stanford University.

       Charles Plessy <charles-debian-nospam@plessy.org>
	   Wrote this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       This program and its manpage are in the public domain.

pc-project 1.12 						    2007-04-04							     PC-PROJECT(1)

Bio::Tools::Run::Alignment::Probcons(3pm)		User Contributed Perl Documentation		 Bio::Tools::Run::Alignment::Probcons(3pm)

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 v5.12.3							    2011-06-18				 Bio::Tools::Run::Alignment::Probcons(3pm)