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 = Bio::Tools::Run::Alignment::Muscle->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.

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

It is recommended you use at least version 3.6. Behaviour with earlier versions is questionable.

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://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 _

new

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

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    :

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;
           $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 (e.g. 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_profile

 Title   : run_profile
 Usage   : $alnfilename = /t/data/cysprot.msa';
           $seqsfilename = 't/data/cysprot.fa';
           $aln = $factory->run_profile($alnfilename,$seqsfilename);
 Function: Perform a profile alignment on a MSA to include more seqs
 Returns : Reference to a SimpleAlign object containing the
           sequence alignment.
 Args    : Name of a file containing the fasta MSA and name of a file
           containing a set of unaligned fasta sequences
 Comments: This only works for muscle version 3.52.
           Some early versions of the 3.6 sources had a bug that
           caused a segfault with -profile. The attached should fix
           it, if not let Bob Edgar know.

aformat

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

_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

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