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   : 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)

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

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

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

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

Methods code

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;

}

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 _add_band {

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

}

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 migrate {

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

}

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 log10 {

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

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
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  bioperl-bugs@bioperl.org
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Email allenday@ucla.edu

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