Bio::Tools::Run::Alignment::Muscle(3)

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

SYNOPSIS
  # Build a muscle alignment factory
  $factory = new Bio::Tools::Run::Alignment::Muscle (@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.

DESCRIPTION
Muscle is Robert Edgar's progressive alignment program. You can get it and see information about it at this URL http://www.drive5.com/muscle

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

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

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

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://bio.perl.org/MailList.html - About the mailing lists

  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://bugzilla.open-bio.org/

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, obtiained from ENV variable.
 Returns:  string
 Args    :

  new
 Title   : new
 Usage   : my $muscle = Bio::Tools::Run::Alignment::Muscle->new();
 Function: Constructor
 Returns : Bio::Tools::Run::Alignment::Muscle
 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 muscle program
 Example :
 Returns : nothing; muscle 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 muscle

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