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Summary

Bio::Tools::Gel - Calculates relative electrophoretic migration distances

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

    #An example of a virtual restriction digest and subsequent gel run
    use Bio::Seq;
    use Bio::Tools::RestrictionEnzyme;
    use Bio::Tools::Gel;

    my $d = 'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG';
    my $seq1 = Bio::Seq->new(-id=>'groundhog day',-seq=>$d);
    my $EcoRI = Bio::Tools::RestrictionEnzyme->new(-NAME=>'EcoRI');
    my @cuts = $EcoRI->cut_seq($seq);

    my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10);
    my %bands = $gel->bands;
    foreach my $band (keys %bands){
      print $band,"\t",$bands{$band},"\n";
    }

    #prints:
    #25      26.0205999132796
    #10      30
    #20      26.9897000433602

Description

This takes a set of sequences or Bio::Seq objects, and calculates their
respective migration distances using:
distance = dilation * (4 - log10(length(dna));
Source: Molecular Cloning, a Laboratory Manual. Sambrook, Fritsch, Maniatis.
CSHL Press, 1989.
Bio::Tools::Gel currently calculates migration distances based solely on
the length of the nucleotide sequence. Secondary or tertiary structure,
curvature, and other biophysical attributes of a sequence are currently
not considered. Polypeptide migration is currently not supported.

Methods

Methods description

 Title   : _add_band
 Usage   : $gel->_add_band($seq);
 Function: Adds a new band to the gel.
 Returns : 
 Args    : Bio::Seq object

 Title   : add_band
 Usage   : $gel->add_band($seq);
 Function: Calls _add_band with a (possibly created) Bio::Seq object.
 Returns : 
 Args    : Bio::Seq, scalar sequence, or list of either/both.

 Title   : bands
 Usage   : $gel->bands;
 Function: Calculates migration distances of sequences.
 Returns : hash of (seq_id => distance)
 Args    :

 Title   : dilate
 Usage   : $gel->dilate(1);
 Function: Sets/retrieves the dilation factor.
 Returns : dilation factor 
 Args    : Float or none

 Title   : log10
 Usage   : log10($n);
 Function: returns base 10 log of $n.
 Returns : float
 Args    : float

 Title   : new
 Usage   : my $gel = new Bio::Tools::Gel(-seq => $sequence,-dilate => 3);
 Function: Initializes a new Gel
 Returns : Bio::Tools::Gel
 Args    : -seq      => Bio::Seq(s), scalar(s) or list of either/both 
                        (default: none)
           -dilate   => Expand band migration distances (default: 1)

Methods code

sub _add_band {

  my($self,$arg) = @_;  
  if( defined $arg) {
      push (@{$self->{'bands'}},$arg);
  }

}

sub add_band {

  my($self,$args) = @_;

  foreach my $arg (@$args){
      my $seq;
      if( ! ref($arg) ) {
	  if( $arg =~ /^\d+/ ) {
	      $seq= Bio::PrimarySeq->new(-seq=>"N"x$arg, -id => $arg);
	  } else {
	      $seq= Bio::PrimarySeq->new(-seq=>$arg,-id=>length($arg));
	  }
      } elsif( $arg->isa('Bio::PrimarySeqI') ) {
	  $seq = $arg;
      } 

    $seq->validate_seq or $seq->throw("invalid symbol in sequence".$seq->seq()."\n");
    $self->_add_band($seq);
  }

}

sub bands {

  my $self = shift;
  $self->throw("bands() is read-only") if @_;

  my %bands = ();
  
  foreach my $band (@{$self->{bands}}){
      my $distance = $self->dilate * migrate($band->length);
      $bands{$band->id} = $distance;
  }

  return %bands;

}

sub dilate {

  my($self,$arg) = @_;
  return $self->{dilate} unless $arg;
  $self->throw("-dilate should be numeric") if defined $arg and $arg =~ /[^e\d\.]/;
  $self->{dilate} = $arg;
  return $self->{dilate};

}

sub log10 {

    my $n = shift;
    return log($n)/log(10);
}

1;

}

sub migrate {

  my ($self,$arg) = @_;
  $arg = $self unless $arg;
  if ( $arg ) {
      return 4 - log10($arg);
  } else { return 0; }

}

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($seqs,$dilate) = $self->_rearrange([qw(SEQ DILATE)],
					  @args);
  if( ! ref($seqs)  ) {
      $self->add_band([$seqs]);
  } elsif( ref($seqs) =~ /array/i ||
	   $seqs->isa('Bio::PrimarySeqI') ) {
      $self->add_band($seqs);
  } 
  $self->dilate($dilate || 1);
  
  return $self;

}

General documentation

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
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of the bugs and their resolution. Bug reports can be submitted via
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  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

Email allenday@ucla.edu

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _