NAME

Bio::Tools::Run::Alignment::Amap - Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program

SYNOPSIS

  # Build a muscle alignment factory
  $factory = Bio::Tools::Run::Alignment::Amap->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 amap with training, try something like:

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

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

DESCRIPTION

Amap uses a Sequence Annealing algorithm which is an incremental method for building multiple alignments. You can get it and see information about it at this URL http://bio.math.berkeley.edu/amap/

Helping the module find your executable

FIXME: Amap uses the same parameters as Probcons, plus a few others. I haven't had time to check all the changes from the Probcons.pm runnable. Feel free to do it.

You will need to enable Amap to find the amap program. This can be done in (at least) three ways:

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

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

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 - Albert Vilella

Email foo@bar.com

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 $amap = Bio::Tools::Run::Alignment::Amap->new();
 Function: Constructor
 Returns : Bio::Tools::Run::Alignment::Amap
 Args    : -outfile_name => $outname

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 amap program
 Example :
 Returns : nothing; amap 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 amap

_setinput

 Title   :  _setinput
 Usage   :  Internal function, not to be called directly        
 Function:  Create input file for amap program
 Example :
 Returns : name of file containing amap 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 amap program
 Example :
 Returns : parameter string to be passed to amap
           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 = $amap->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   : $amap->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