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

NAME

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

SYNOPSIS

# Build a MAFFT alignment factory
$factory = Bio::Tools::Run::Alignment::MAFFT->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);

#There are various additional options available.

DESCRIPTION

You can get MAFFT from http://mafft.cbrc.jp/alignment/software/. "fftnsi" is the default method for Mafft version 4 in this implementation.

See Bio::Tools::Run::Alignment::Clustalw for a description on how to specify parameters to the underlying alignment program. See the MAFFT manual page for a description of the MAFFT parameters.

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://redmine.open-bio.org/projects/bioperl/

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

_version6

Title   : _version6
Usage   : Internal function, not to be called directly
Function: Check if the version of MAFFT is 6
Example :
Returns : Boolean
Args    : None

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