Bio::Tools::Run::Alignment::MAFFT.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::Alignment::MAFFT - run the MAFFT alignment tools

SYNOPSIS

   use Bio::Tools::Run::Alignment::MAFFT;
 
 

DESCRIPTION

You can get MAFFT from http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft4/ <http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft4/>. ``fftnsi'' is the default in this implementation.

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/MailList.html - 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://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl.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
 
 

executable

  Title   : executable
  Usage   : my $exe = $blastfactory->executable('blastall');
  Function: Finds the full path to the 'codeml' executable
  Returns : string representing the full path to the exe
  Args    : [optional] name of executable to set path to 
            [optional] boolean flag whether or not warn when exe is not found
 
 

program_path

  Title   : program_path
  Usage   : my $path = $factory->program_path();
  Function: Builds path for executable 
  Returns : string representing the full path to the exe
  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 analysis 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    : array ref of Bio::PrimarySeqI objects OR
            filename of sequences to run with
 
 

align

  Title   : align
  Usage   :
         $inputfilename = 't/data/cysprot.fa';
         $aln = $factory->align($inputfilename);
 or
         $seq_array_ref = \@seq_array; 
         # @seq_array is an 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 tcoffee program
  Example :
  Returns : nothing; tcoffee 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 tcoffee
 
 

_setinput

  Title   :  _setinput
  Usage   :  Internal function, not to be called directly
  Function:  Create input file for mafft programs
  Example :
  Returns : name of file containing mafft data input 
  Args    : Seq or Align object reference or input file name
 
 

_setparams

  Title   :  _setparams
  Usage   :  Internal function, not to be called directly        
  Function:  Create parameter inputs for mafft program
  Example :
  Returns : parameter string to be passed to mafft program
  Args    : name of calling object
 
 

methods

  Title   : methods
  Usage   : my @methods = $self->methods()
  Function: Get/Set Alignment methods - NOT VALIDATED
  Returns : array of strings
  Args    : arrayref of strings
 
 

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 = $mafft->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   : $mafft->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