/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Alignment::Amap

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