diff variant_effect_predictor/Bio/Tools/Gel.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Gel.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,237 @@
+# $Id: Gel.pm,v 1.6 2002/10/22 07:45:22 lapp Exp $
+# BioPerl module for Bio::Tools::Gel
+# Copyright Allen Day <[e-mail]>
+# 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.
+
+  [e-mail]            - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Allen Day
+
+Email [e-mail]
+
+=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;