Raw content of Bio::Tools::Gel
<![CDATA[# $Id: Gel.pm,v 1.6 2002/10/22 07:45:22 lapp Exp $
# BioPerl module for Bio::Tools::Gel
# Copyright Allen Day <allenday@ucla.edu>
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Gel - Calculates relative electrophoretic migration distances
=head1 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
=head1 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.
=head1 FEEDBACK
=head2 Mailing Lists
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/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Allen Day
Email allenday@ucla.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Gel;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::PrimarySeq;
@ISA = qw(Bio::Root::Root);
=head2 new
Title : new
Usage : my $gel = new Bio::Tools::Gel(-seq => $sequence,-dilate => 3);
Function: Initializes a new Gel
Returns : Bio::Tools::Gel
Args : -seq => Bio::Seq(s), scalar(s) or list of either/both
(default: none)
-dilate => Expand band migration distances (default: 1)
=cut
sub new {
my($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;
}
=head2 add_band
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.
=cut
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);
}
}
=head2 _add_band
Title : _add_band
Usage : $gel->_add_band($seq);
Function: Adds a new band to the gel.
Returns :
Args : Bio::Seq object
=cut
sub _add_band {
my($self,$arg) = @_;
if( defined $arg) {
push (@{$self->{'bands'}},$arg);
}
}
=head2 dilate
Title : dilate
Usage : $gel->dilate(1);
Function: Sets/retrieves the dilation factor.
Returns : dilation factor
Args : Float or none
=cut
sub dilate {
my($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; }
}
=head2 bands
Title : bands
Usage : $gel->bands;
Function: Calculates migration distances of sequences.
Returns : hash of (seq_id => distance)
Args :
=cut
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} = $distance;
}
return %bands;
}
=head2 log10
Title : log10
Usage : log10($n);
Function: returns base 10 log of $n.
Returns : float
Args : float
=cut
#from programming perl
sub log10 {
my $n = shift;
return log($n)/log(10);
}
1;
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