Bio::Tools::Run Mdust
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Summary
Mdust - Perl extension for Mdust nucleotide filtering
Package variables
No package variables defined.
Included modules
Bio::Root::IO
Bio::Root::Root
Bio::SeqFeature::Generic
Bio::SeqIO
Bio::Tools::Run::WrapperBase
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  use Bio::Tools::Run::Mdust;
my $mdust = Bio::Tools::Run::Mdust->new();
$mdust->run($bio_seq_object);
Description
Perl wrapper for the nucleic acid complexity filtering program
mdust as available from TIGR via
http://www.tigr.org/tdb/tgi/software/. Takes a Bio::SeqI or
Bio::PrimarySeqI object of type DNA as input.
If a Bio::Seq::RichSeqI is passed then the low-complexity regions will
be added to the feature table of the target object as
Bio::SeqFeature::Generic items with primary tag = 'Excluded' .
Otherwise a new target object will be returned with low-complexity
regions masked (by N's or other character as specified by maskchar()).
The mdust executable must be in a directory specified with either the
PATH or MDUSTDIR environment variable.
Methods
newDescriptionCode
runDescriptionCode
program_dir
No description
Code
program_name
No description
Code
_run_mdust
No description
Code
targetDescriptionCode
_set_target
No description
Code
_maskedfile
No description
Code
_parse_coords
No description
Code
maskcharDescriptionCode
DESTROY
No description
Code
AUTOLOAD
No description
Code
Methods description
newcode    nextTop
  Title		: new
Usage : my $mdust = Bio::Tools::Run::Mdust->new( -target => $target_bioseq)
Purpose : Create a new mdust object
Returns : A Bio::Seq object
Args : target - Bio::Seq object for masking - alphabet MUST be DNA.
wsize - word size for masking (default = 3)
cutoff - cutoff score for masking (default = 28)
maskchar - character for replacing masked regions (default = N)
coords - boolean - indicate low-complexity regions as
Bio::SeqFeature::Generic
objects with primary tag 'Excluded',
do not change sequence (default 0)
tmpdir - directory for storing temporary files
debug - boolean - toggle debugging output,
do not remove temporary files
Notes : All of the arguments can also be get/set with their own accessors, such as:
my $wsize = $mdust->wsize();
When processing multiple sequences, call Bio::Tools::Run::Mdust->new() once then pass each sequence as an argument to the target() or run() methods.
runcodeprevnextTop
  Title		: run
Usage : $mdust->run();
Purpose : Run mdust on the target sequence
Args : target (optional) - Bio::Seq object of alphabet DNA for masking
Returns : Bio::Seq object with masked sequence or low-complexity regions added to feature table.
targetcodeprevnextTop
  Title		: target
Usage : $mdust->target($bio_seq)
Purpose : Set/get the target (sequence to be filtered).
Returns : Target Bio::Seq object
Args : Bio::SeqI or Bio::PrimarySeqI object using the DNA alphabet (optional)
Note : If coordinate parsing is selected ($mdust->coords = 1) then target
MUST be a Bio::Seq::RichSeqI object. Passing a RichSeqI object automatically
turns on coordinate parsing.
maskcharcodeprevnextTop
  Title		: maskchar
Usage : $mdust->maskchar('N')
Purpose : Set/get the character for masking low-complexity regions
Returns : True on success
Args : Either N (default), X or L (lower case)
Methods code
newdescriptionprevnextTop
sub new {
    my ($proto, @args) = @_;
    my $pkg = ref($proto) || $proto;
    my %args;

    my $self = { wsize		=> undef,
		 cutoff		=> undef,
		 maskchar	=> undef,
		 coords		=> 0,
	     };

    bless ($self, $pkg);

    @args{@ARGNAMES} = $self->_rearrange(\@ARGNAMES, @args); 

    # load target first since it requires special handling
$self->target($args{'TARGET'}) if ($args{'TARGET'}); # package settings
$self->{'coords'} = $args{'COORDS'} if (defined $args{'COORDS'}); $self->{'tmpdir'} = $args{'TMPDIR'} || $ENV{'TMPDIR'} || $ENV{'TMP'} || '.'; # mdust options
$self->{'wsize'} = $args{'WSIZE'} if (defined $args{'WSIZE'}); $self->{'cutoff'} = $args{'CUTOFF'} if (defined $args{'CUTOFF'}); $self->{'maskchar'} = $args{'MASKCHAR'} if (defined $args{'CUTOFF'}); # set debugging
$self->verbose($args{'DEBUG'}); return $self;
}
rundescriptionprevnextTop
sub run {
    my ($self, $target) = @_;

    if ($target) {
	$self->target($target);
    }

    return $self->_run_mdust;
}
program_dirdescriptionprevnextTop
sub program_dir {
        return Bio::Root::IO->catfile($ENV{MDUSTDIR}) if $ENV{MDUSTDIR};
}
program_namedescriptionprevnextTop
sub program_name {
    return $PROGRAMNAME;
}
_run_mdustdescriptionprevnextTop
sub _run_mdust {
    # open a pipe to the mdust command.  Pass in sequence(s?) as fasta 
# files on STDIN, recover filtered seqs on STDOUT
my ($self) = @_; my $target = $self->target or warn "No target sequence specified\n" && return undef; # make sure program is available - doesn't seem to check
#my $executable = $self->executable('mdust', 1);
# add options
my $mdust_cmd = $self->program_path; $mdust_cmd .= " -w " . $self->wsize if (defined $self->wsize); $mdust_cmd .= " -v " . $self->cutoff if (defined $self->cutoff); $mdust_cmd .= " -m " . $self->maskchar if (defined $self->maskchar); $mdust_cmd .= " -c" if ($self->coords); print STDERR "Running mdust: $mdust_cmd\n" if ($self->debug); my $maskedfile = $self->_maskedfile; eval { my $pid = open (MDUST, "| $mdust_cmd > $maskedfile"); # bind STDIN of mdust to filehandle
local $| = 1; my $seqout = Bio::SeqIO->new(-fh =>\* MDUST, -format => 'Fasta'); $seqout->write_seq($target); close MDUST; # need to do this to get output to flush!
}; $self->throw($@) if ($@); my $rval; if ($self->coords) { $self->_parse_coords($maskedfile); $rval = $self->target; } else { # replace original seq w/ masked seq
my $seqin = Bio::SeqIO->new(-file=>$maskedfile, -format => 'Fasta'); $rval = $seqin->next_seq } unlink $maskedfile unless $self->save_tempfiles; return $rval;
}
targetdescriptionprevnextTop
sub target {
    my ($self, $targobj) = @_;

    if ($targobj) {
	return $self->_set_target($targobj);
    }
    else {
	return $self->{'target'};
    }
}
_set_targetdescriptionprevnextTop
sub _set_target {
    my ($self, $targobj) = @_;

    unless ($targobj->isa('Bio::SeqI') or ($targobj->isa('Bio::PrimarySeqI'))) {
	$self->throw( -text => "Target must be passed as a Bio::SeqI or Bio::PrimarySeqI object",
		      -class => 'Bio::Root::BadParameter',
		      -value => $targobj );
    } 


    if ($self->coords) {
	unless ($targobj->isa('Bio::Seq::RichSeqI')) {
	    $self->throw( -text => "Target must be passed as a Bio::Seq::RichSeqSeqI object when coords == 1",
			  -class => 'Bio::Root::BadParameter',
			  -value => $targobj );
	} 
    }	
    elsif ($targobj->isa('Bio::Seq::RichSeqI')) {
	$self->coords(1);
    }


    unless ($targobj->alphabet eq 'dna') {
	$self->throw( -text => "Target must be a DNA sequence",
		      -class => 'Bio::Root::BadParameter',
		      -value => $targobj );
    }

    $self->{'target'} = $targobj;
    return 1;
}
_maskedfiledescriptionprevnextTop
sub _maskedfile {
    my ($self, $file) = @_;
    my $tmpdir = $self->tempdir;

    if ($file) {
	$self->{'maskedfile'} = $file;
	# add some sanity chex for writability?
} elsif (!$self->{'maskedfile'}) { ($self->{'maskedfh'},$self->{'maskedfile'}) = $self->io->tempfile(-dir=>$self->tempdir()); } return $self->{'maskedfile'};
}
_parse_coordsdescriptionprevnextTop
sub _parse_coords {
    my ($self, $file) = @_;
    my $target = $self->target;
    open(FILE, $file) or die "Unable to open $file: $!";
    while (<FILE>) {
	chomp;
	s/\r//;
	my ($seq, $length, $mstart, $mstop) = split(/\t/);

	# add masked region as a SeqFeature in target
my $masked = Bio::SeqFeature::Generic->new( -start => $mstart, -end => $mstop, ); $masked->primary_tag('Excluded'); $masked->source_tag('mdust'); $target->add_SeqFeature($masked); } return 1;
}
maskchardescriptionprevnextTop
sub maskchar {
    my ($self, $maskchar) = @_;

    return $self->{'maskchar'} unless (defined $maskchar);

    unless ( grep {$maskchar eq $_} @MASKCHARS ) {
	$self->throw( -text => "maskchar must be one of N, X or L",
		      -class => 'Bio::Root::BadParameter',
		      -value => $maskchar );
    }
    $self->{'maskchar'} = $maskchar;

    1;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self= shift;
    unless ( $self->save_tempfiles ) {
        $self->cleanup();
    }
    $self->SUPER::DESTROY();
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
    my ($self, $value) = @_;
    my $name = $AUTOLOAD;
    $name =~ s/.+:://;

    return if ($name eq 'DESTROY');


    if (defined $value) {
	$self->{$name} = $value;
    }

    unless (exists $self->{$name}) {
	warn "Attribute $name not defined for ", ref($self), "\n" if ($self->debug);
  	return undef;
    }

    return $self->{$name};
}

1;
}
General documentation
SEE ALSOTop
mdust,
Bio::PrimarySeq,
Bio::Seq::RichSeq,
Bio::SeqFeature::Generic
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
the Bioperl mailing list. 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
of the bugs and their resolution. Bug reports can be submitted via
the web:
  http://bugzilla.open-bio.org/
AUTHORTop
Donald Jackson (donald.jackson@bms.com)
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _