Bio::Tools::Run::Alignment Muscle
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Summary
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
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
  # 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. 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;
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
newDescriptionCode
AUTOLOAD
No description
Code
error_stringDescriptionCode
versionDescriptionCode
runDescriptionCode
alignDescriptionCode
profileDescriptionCode
_runDescriptionCode
_setinputDescriptionCode
_setparamsDescriptionCode
aformatDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
newcodeprevnextTop
 Title   : new
Usage : my $muscle = Bio::Tools::Run::Alignment::Muscle->new();
Function: Constructor
Returns : Bio::Tools::Run::Alignment::Muscle
Args : -outfile_name => $outname
error_stringcodeprevnextTop
 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)
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 : Arrayref of Bio::PrimarySeqI objects or
a filename to run on
aligncodeprevnextTop
 Title   : align
Usage :
$inputfilename = 't/data/cysprot.fa';
$aln = $factory->align($inputfilename);
or
$seq_array_ref = \@seq_array;
# @seq_array is 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.
profilecodeprevnextTop
 Title   : profile
Usage :
$alnfilename = /t/data/cysprot.msa';
$seqsfilename = 't/data/cysprot.fa';
$aln = $factory->profile($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.
_runcodeprevnextTop
 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
_setinputcodeprevnextTop
 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
_setparamscodeprevnextTop
 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
aformatcodeprevnextTop
 Title   : aformat
Usage : my $alignmentformat = $self->aformat();
Function: Get/Set alignment format
Returns : string
Args : string
Methods code
BEGINTop
BEGIN {
    %DEFAULTS = ( 'AFORMAT' => 'fasta' );
    @MUSCLE_PARAMS = qw(IN OUT TREE1 LOG LOGA SCOREFILE GAPOPEN 
			MAXMB MAXHOURS MAXITERS KBAND IN1 IN2);
    @MUSCLE_SWITCHES = qw(QUIET DIAGS REFINE STABLE GROUP 
			  CLW CLWSTRICT MSF);

# Authorize attribute fields
foreach my $attr ( @MUSCLE_PARAMS, @MUSCLE_SWITCHES ) { $OK_FIELD{$attr}++;
}
program_namedescriptionprevnextTop
sub program_name {
        return 'muscle';
}
program_dirdescriptionprevnextTop
sub program_dir {
        return Bio::Root::IO->catfile($ENV{MUSCLEDIR}) if $ENV{MUSCLEDIR};
}
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;
    my( @muscle_args, @obj_args);
    while( my $arg = shift @args ) {
	if( $arg =~ /^-/ ) {
	    push @obj_args, $arg, shift @args;
	} else {
	    push @muscle_args,$arg, shift @args;
	}
    }
    my $self = $class->SUPER::new(@obj_args);
    
    my ($on) = $self->_rearrange([qw(OUTFILE_NAME)],@obj_args);
    
    $self->outfile_name($on || '');
    my ($attr, $value);    
    $self->aformat($DEFAULTS{'AFORMAT'});

    while ( @muscle_args)  {
	$attr =   shift @muscle_args;
	$value =  shift @muscle_args;
	next if( $attr =~ /^-/); # don't want named parameters
$self->$attr($value); } $self->aformat('msf') if $self->msf; $self->aformat('clustalw') if $self->clw || $self->clwstrict; if( defined $self->out ) { $self->outfile_name($self->out); } return $self;
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    # aliasing
$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 undef unless $exe = $self->executable;
    my $string = `$exe 2>&1` ;

    $string =~ /MUSCLE\s+v(\d+\.\d+)/m;
    return $1 || undef;
}
rundescriptionprevnextTop
sub run {
    my $self = shift;
    return $self->align(shift);
}
aligndescriptionprevnextTop
sub align {
    my ($self,$input) = @_;
    # Create input file pointer
$self->io->_io_cleanup(); my $infilename; if( defined $input ) { $infilename = $self->_setinput($input); } elsif( defined $self->in ) { $infilename = $self->_setinput($self->in); } else { $self->throw("No inputdata provided\n"); } if (! $infilename) { $self->throw("Bad input data or less than 2 sequences in $input !"); } my $param_string = $self->_setparams(); # run muscle
return &_run($self, $infilename, $param_string);
}
profiledescriptionprevnextTop
sub profile {
    my ($self,$alnfilename,$seqsfilename) = @_;
    # Create input file pointer
$self->io->_io_cleanup(); if ($self->version ne '3.52') { $self->throw("profile does not work for this version of muscle\n"); } my $infilename; if( defined $alnfilename ) { if (! ref $alnfilename) { # check that file exists or throw
$infilename = $alnfilename; unless (-e $infilename) {return 0;} # let's peek and guess
open(IN,$infilename) || $self->throw("Cannot open $infilename"); my $header; while( defined ($header = <IN>) ) { last if $header !~ /^\s+$/; } close(IN); if ( $header !~ /^>\s*\S+/ ){ $self->throw("Need to provide a FASTA format file to muscle profile!"); } } } else { $self->throw("No inputdata provided\n"); } if (! $infilename) { $self->throw("Bad input data or less than 2 sequences in $infilename !"); } if( defined $seqsfilename ) { if (! ref $seqsfilename) { # check that file exists or throw
$infilename = $seqsfilename; unless (-e $infilename) {return 0;} # let's peek and guess
open(IN,$infilename) || $self->throw("Cannot open $infilename"); my $header; while( defined ($header = <IN>) ) { last if $header !~ /^\s+$/; } close(IN); if ( $header !~ /^>\s*\S+/ ){ $self->throw("Need to provide a FASTA format file to muscle profile!"); } } } else { $self->throw("No inputdata provided\n"); } if (! $infilename) { $self->throw("Bad input data or less than 2 sequences in $infilename !"); } my $param_string = $self->_setparams(); # run muscle
$self->{_profile} = 1; return &_run($self, "$alnfilename -in2 $seqsfilename", $param_string);
}
_rundescriptionprevnextTop
sub _run {
    my ($self,$infilename,$params) = @_;
    my $commandstring;
    if ($self->{_profile}) {
        $commandstring = $self->executable." -profile -in1 $infilename $params";
        $self->{_profile} = 0;
    } else {
        $commandstring = $self->executable." -in $infilename $params";
    }

    $self->debug( "muscle command = $commandstring\n ");

    my $status = system($commandstring);
    my $outfile = $self->outfile_name(); 
    if( !-e $outfile || -z $outfile ) {
	$self->warn( "Muscle call crashed: $? [command $commandstring]\n");
	return undef;
    }

    my $in  = Bio::AlignIO->new('-file'   => $outfile, 
				'-format' => $self->aformat);
    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 $input) {return 0;} # let's peek and guess
open(IN,$infilename) || $self->throw("Cannot open $infilename"); my $header; while( defined ($header = <IN>) ) { last if $header !~ /^\s+$/; } close(IN); if ( $header !~ /^>\s*\S+/ ){ $self->throw("Need to provide a FASTA format file to muscle!"); } return ($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 undef; } 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 ($attr, $value,$param_string);
    $param_string = '';
    my $laststr;
    for  $attr ( @MUSCLE_PARAMS ) {
	$value = $self->$attr();
	next unless (defined $value);	
	my $attr_key = lc $attr;
        $attr_key = ' -'.$attr_key;
        $param_string .= $attr_key .' '.$value;

    }
    for  $attr ( @MUSCLE_SWITCHES) {
 	$value = $self->$attr();
 	next unless ($value);
 	my $attr_key = lc $attr; #put switches in format expected by tcoffee
$attr_key = ' -'.$attr_key; $param_string .= $attr_key ; } # Set default output file if no explicit output file selected
unless ($self->outfile_name ) { my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir()); close($tfh); undef $tfh; $self->outfile_name($outfile); } $param_string .= " -out ".$self->outfile_name; if ($self->quiet() || $self->verbose < 0) { $param_string .= ' 2> /dev/null'; } return $param_string;
}
aformatdescriptionprevnextTop
sub aformat {
    my $self = shift;
    $self->{'_aformat'} = shift if @_;
    return $self->{'_aformat'};
}
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/wiki/Mailing_lists - 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-dot-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 = $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
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 : $muscle->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