| Bio::Tools::Run::Alignment::MAFFT(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Alignment::MAFFT(3pm) |
Bio::Tools::Run::Alignment::MAFFT - run the MAFFT alignment tools
# 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.
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None
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
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
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
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)
Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none
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
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.
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
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
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
Title : methods Usage : my @methods = $self->methods() Function: Get/Set Alignment methods - NOT VALIDATED Returns : array of strings Args : arrayref of strings
Title : _version6 Usage : Internal function, not to be called directly Function: Check if the version of MAFFT is 6 Example : Returns : Boolean Args : None
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)
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)
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
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
Title : cleanup Usage : $mafft->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none
| 2023-01-22 | perl v5.36.0 |