Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


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


   # 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",
   #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",
   $aln = $factory->align($seq_array_ref);


Probcons is a Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences. You can get it and see information about it at this URL

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;


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.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

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:

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


  Title   : program_name
  Usage   : $factory->program_name()
  Function: holds the program name
  Returns:  string
  Args    : None


  Title   : program_dir
  Usage   : $factory->program_dir(@params)
  Function: returns the program directory, obtained from ENV variable.
  Returns:  string
  Args    :


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


  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)


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


  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


  Title   : align
  Usage   :
         $inputfilename = 't/data/cysprot.fa';
         $aln = $factory->align($inputfilename);
         $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.


  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


  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


  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


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

Bio::Tools::Run::BaseWrapper methods


  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)


  Title   : save_tempfiles
  Usage   : $obj->save_tempfiles($newval)
  Returns : value of save_tempfiles
  Args    : newvalue (optional)


  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


  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


  Title   : cleanup
  Usage   : $probcons->cleanup();
  Function: Will cleanup the tempdir directory
  Returns : none
  Args    : none


  Title   : io
  Usage   : $obj->io($newval)
  Function:  Gets a L<Bio::Root::IO> object
  Returns : L<Bio::Root::IO>
  Args    : none