Bio::Tools::Run::Alignment MAFFT
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Summary
Bio::Tools::Run::Alignment::MAFFT - run the MAFFT alignment tools
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Factory::ApplicationFactoryI
Bio::Root::IO
Bio::Root::Root
Bio::Seq
Bio::SeqIO
Bio::SimpleAlign
Bio::Tools::Run::WrapperBase
Inherit
Bio::Factory::ApplicationFactoryI Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  use Bio::Tools::Run::Alignment::MAFFT;
Description
You can get MAFFT from
http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft4/.
"fftnsi" is the default in this implementation.
Methods
BEGIN Code
program_nameDescriptionCode
executableDescriptionCode
program_pathDescriptionCode
program_dirDescriptionCode
new
No description
Code
AUTOLOAD
No description
Code
error_stringDescriptionCode
versionDescriptionCode
runDescriptionCode
alignDescriptionCode
_runDescriptionCode
_setinputDescriptionCode
_setparamsDescriptionCode
methodsDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
executablecodeprevnextTop
 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_pathcodeprevnextTop
 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_dircodeprevnextTop
 Title   : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
error_stringcodeprevnextTop
 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)
versioncodeprevnextTop
 Title   : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
runcodeprevnextTop
 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
aligncodeprevnextTop
 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.
_runcodeprevnextTop
 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
_setinputcodeprevnextTop
 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
_setparamscodeprevnextTop
 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
methodscodeprevnextTop
 Title   : methods
Usage : my @methods = $self->methods()
Function: Get/Set Alignment methods - NOT VALIDATED
Returns : array of strings
Args : arrayref of strings
Methods code
BEGINTop
BEGIN {
    %DEFAULTS = ( 'OUTPUT' => 'fasta',
		  'METHOD' => 'fftnsi',
		  'CYCLES' => 2);
    @MAFFT_PARAMS =qw( METHOD CYCLES );
    @MAFFT_SWITCHES = qw( NJ ALL_POSITIVE);
    @OTHER_SWITCHES = qw(QUIET ALIGN OUTPUT OUTFILE);
    @MAFFT_ALN_METHODS = qw(fftnsi fftns nwnsi nwns fftnsrough nwnsrough);
    # Authorize attribute fields
foreach my $attr ( @MAFFT_SWITCHES,@MAFFT_PARAMS,@OTHER_SWITCHES ) { $OK_FIELD{$attr}++;
}
program_namedescriptionprevnextTop
sub program_name {
        return 'mafft';
}
executabledescriptionprevnextTop
sub executable {
   my ($self, $exename, $exe,$warn) = @_;
   $exename = $self->program_name unless (defined $exename );

   if( defined $exe && -x $exe ) {
     $self->{'_pathtoexe'}->{$exename} = $exe;
   }
   unless( defined $self->{'_pathtoexe'}->{$exename} ) {
       my $f = $self->program_path($exename);	    
       $exe = $self->{'_pathtoexe'}->{$exename} = $f if(-e $f && -x $f );
        
       #  This is how I meant to split up these conditionals --jason
# if exe is null we will execute this (handle the case where
# PROGRAMDIR pointed to something invalid)
unless( $exe ) { # we didn't find it in that last conditional
if( ($exe = $self->io->exists_exe($exename)) && -x $exe ) { $self->{'_pathtoexe'}->{$exename} = $exe; } else { $self->warn("Cannot find executable for $exename") if $warn; $self->{'_pathtoexe'}->{$exename} = undef; } } } return $self->{'_pathtoexe'}->{$exename};
}
program_pathdescriptionprevnextTop
sub program_path {
    my ($self,$program_name) = @_;
    my @path;
    push @path, $self->program_dir if $self->program_dir;
    push @path, $program_name .($^O =~ /mswin/i ?'.exe':'');

    return Bio::Root::IO->catfile(@path);
}
program_dirdescriptionprevnextTop
sub program_dir {
        return File::Spec->rel2abs($ENV{MAFFTDIR}) if $ENV{MAFFTDIR};
}
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($attr, $value);    
    
    while (@args)  {
	$attr =   shift @args;
	$value =  shift @args;
	next if( $attr =~ /^-/); # don't want named parameters
$self->$attr($value); } $self->output($DEFAULTS{'OUTPUT'}) unless( $self->output ); $self->method($DEFAULTS{'METHOD'}) unless( $self->method ); return $self;
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    # aliasing
$attr = 'OUTFILE' if $attr eq 'OUTFILE_NAME'; $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr}; $self->{$attr} = shift if @_; return $self->{$attr};
}
error_stringdescriptionprevnextTop
sub error_string {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'error_string'} = $value;
    }
    return $self->{'error_string'};
}
versiondescriptionprevnextTop
sub version {
    my ($self) = @_;
    my $exe;
    return unless $exe = $self->executable;
    # this is a bit of a hack, but MAFFT is just a gawk script
# so we are actually grepping the scriptfile
# UPDATE (Torsten Seemann)
# it now seems to be a 'sh' script and the format has changed
# slightly. i've tried to make the change compatible with both...
# version="v5.860 (2006/06/12)"; export version
if( open(my $NAME, "grep 'export version' $exe | ") ) { while(<$NAME>) { if( /version.*?([\d.a-z]+)\s+/ ) { return $1; } } $self->warn("No version found"); close($NAME); } else { $self->warn("$!"); } return;
}
rundescriptionprevnextTop
sub run {
   my ($self,$seqs) = @_;
   return $self->align($seqs);
}
aligndescriptionprevnextTop
sub align {
    my ($self,$input) = @_;
    # Create input file pointer
$self->io->_io_cleanup(); my ($infilename,$type) = $self->_setinput($input); if (! $infilename) { $self->throw("Bad input data or less than 2 sequences in $input !"); } my ($param_string,$outstr) = $self->_setparams(); # run mafft
return &_run($self, $infilename, $param_string,$outstr);
}
_rundescriptionprevnextTop
sub _run {
    my ($self,$infilename,$paramstr,$outstr) = @_;
     my $commandstring = $self->executable($self->method)." $paramstr $infilename $outstr";
    
    $self->debug( "mafft command = $commandstring\n ");

    my $status = system($commandstring);
    my $outfile = $self->outfile(); 
    if( !-e $outfile || -z $outfile ) {
	$self->warn( "MAFFT call crashed: $? [command $commandstring]\n");
	return;
    }
    
    my $in  = Bio::AlignIO->new('-file' => $outfile, 
				'-format' => $self->output);
    my $aln = $in->next_aln();
    return $aln;
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    if (! ref $input) {
	# check that file exists or throw
$infilename = $input; unless (-e $input) {return 0;} return ($infilename); } elsif (ref($input) =~ /ARRAY/i ) { # $input may be an
# array of BioSeq objects...
# Open temporary file for both reading & writing of array
($tfh,$infilename) = $self->io->tempfile(); if( ! ref($input->[0]) ) { $self->warn("passed an array ref which did not contain objects to _setinput"); return; } elsif( $input->[0]->isa('Bio::PrimarySeqI') ) { $temp = Bio::SeqIO->new('-fh' => $tfh, '-format' => 'fasta'); my $ct = 1; foreach $seq (@$input) { return 0 unless ( ref($seq) && $seq->isa("Bio::PrimarySeqI") ); if( ! defined $seq->display_id || $seq->display_id =~ /^\s+$/) { $seq->display_id( "Seq".$ct++); } $temp->write_seq($seq); } $temp->close(); undef $temp; close($tfh); $tfh = undef; } else { $self->warn( "got an array ref with 1st entry ". $input->[0]. " and don't know what to do with it\n"); } return ($infilename); } else { $self->warn("Got $input and don't know what to do with it\n"); } return 0;
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($self) = @_;
    my ($outfile,$param_string) = ('','');

    # Set default output file if no explicit output file selected
unless (defined($outfile = $self->outfile) ) { my $tfh; ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir()); close($tfh); undef $tfh; $self->outfile($outfile); } my ($attr,$value); for $attr ( @MAFFT_SWITCHES) { $value = $self->$attr(); next unless ($value); my $attr_key = lc $attr; #put switches in format expected by mafft
$attr_key = ' --'.$attr_key; $param_string .= $attr_key ; } my $method = $self->method; $self->throw("no method ") unless defined $method; if( $method !~ /(rough|nsi)$/ && defined $self->cycles) { $param_string .= " ".$self->cycles; } my $outputstr = " 1>$outfile" ; if ($self->quiet() || $self->verbose < 0) { $param_string .= " --quiet"; $outputstr .= ' 2> /dev/null'; } return ($param_string, $outputstr);
}
methodsdescriptionprevnextTop
sub methods {
   my ($self) = shift;
   return @MAFFT_ALN_METHODS;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
 
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 BugsTop
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 StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Bio::Tools::Run::BaseWrapper methodsTop
no_param_checksTop
 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_tempfilesTop
 Title   : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
outfile_nameTop
 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
tempdirTop
 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
cleanupTop
 Title   : cleanup
Usage : $mafft->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
ioTop
 Title   : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO
Args : none