Bio::Tools Gel
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Tools::Gel - Calculates relative electrophoretic migration distances
Package variables
No package variables defined.
Included modules
Bio::PrimarySeq
Inherit
Bio::Root::Root
Synopsis
    use Bio::PrimarySeq;
use Bio::Restriction::Analysis;
use Bio::Tools::Gel;
# get a sequence my $d = 'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG'; my $seq1 = Bio::Seq->new(-id=>'groundhog day',-seq=>$d); # cut it with an enzyme my $ra=Bio::Restriction::Analysis->new(-seq=>$seq1); @cuts = $ra->fragments('EcoRI'), 3; # analyse the fragments in a gel my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10); my %bands = $gel->bands; foreach my $band (sort {$b <=> $a} keys %bands){ print $band,"\t", sprintf("%.1f", $bands{$band}),"\n"; } #prints: #20 27.0 #25 26.0 #10 30.0
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
newDescriptionCode
add_bandDescriptionCode
_add_bandDescriptionCode
dilateDescriptionCode
migrate
No description
Code
bandsDescriptionCode
log10DescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $gel = Bio::Tools::Gel->new(-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)
add_bandcodeprevnextTop
 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.
_add_bandcodeprevnextTop
 Title   : _add_band
Usage : $gel->_add_band($seq);
Function: Adds a new band to the gel.
Returns :
Args : Bio::Seq object
dilatecodeprevnextTop
 Title   : dilate
Usage : $gel->dilate(1);
Function: Sets/retrieves the dilation factor.
Returns : dilation factor
Args : Float or none
bandscodeprevnextTop
 Title   : bands
Usage : $gel->bands;
Function: Calculates migration distances of sequences.
Returns : hash of (seq_id => distance)
Args :
log10codeprevnextTop
 Title   : log10
Usage : log10($n);
Function: returns base 10 log of $n.
Returns : float
Args : float
Methods code
newdescriptionprevnextTop
sub new {
  my($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 $self;
}
add_banddescriptionprevnextTop
sub add_band {
  my($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);
  }
}
_add_banddescriptionprevnextTop
sub _add_band {
  my($self,$arg) = @_;  
  if( defined $arg) {
      push (@{$self->{'bands'}},$arg);
  }
}
dilatedescriptionprevnextTop
sub dilate {
  my($self,$arg) = @_;
  return $self->{dilate} unless $arg;
  $self->throw("-dilate should be numeric") if defined $arg and $arg =~ /[^e\d\.]/;
  $self->{dilate} = $arg;
  return $self->{dilate};
}
migratedescriptionprevnextTop
sub migrate {
  my ($self,$arg) = @_;
  $arg = $self unless $arg;
  if ( $arg ) {
      return 4 - log10($arg);
  } else { return 0; }
}
bandsdescriptionprevnextTop
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;
}
log10descriptionprevnextTop
sub log10 {
    my $n = shift;
    return log($n)/log(10);
} 1;
}
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
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Allen DayTop
Email allenday@ucla.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _