Bio/Tools/Gel.pm

   1 #
   2 # BioPerl module for Bio::Tools::Gel
   3 # Copyright Allen Day <allenday@ucla.edu>
   4 # You may distribute this module under the same terms as perl itself
   5
   6 # POD documentation - main docs before the code
   7
   8 =head1 NAME
   9
  10 Bio::Tools::Gel - Calculates relative electrophoretic migration distances
  11
  12 =head1 SYNOPSIS
  13
  14     use Bio::PrimarySeq;
  15     use Bio::Restriction::Analysis;
  16     use Bio::Tools::Gel;
  17
  18     # get a sequence
  19     my $d = 'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG';
  20     my $seq1 = Bio::Seq->new(-id=>'groundhog day',-seq=>$d);
  21
  22     # cut it with an enzyme
  23     my $ra=Bio::Restriction::Analysis->new(-seq=>$seq1);
  24     @cuts = $ra->fragments('EcoRI'), 3;
  25
  26     # analyse the fragments in a gel
  27     my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10);
  28     my %bands = $gel->bands;
  29     foreach my $band (sort {$b <=> $a} keys %bands){
  30       print $band,"\t", sprintf("%.1f", $bands{$band}),"\n";
  31     }
  32
  33     #prints:
  34     #20   27.0
  35     #25   26.0
  36     #10   30.0
  37
  38 =head1 DESCRIPTION
  39
  40 This takes a set of sequences or Bio::Seq objects, and calculates their
  41 respective migration distances using:
  42     distance = dilation * (4 - log10(length(dna));
  43
  44 Source: Molecular Cloning, a Laboratory Manual. Sambrook, Fritsch, Maniatis.
  45 CSHL Press, 1989.
  46
  47 Bio::Tools::Gel currently calculates migration distances based solely on
  48 the length of the nucleotide sequence.  Secondary or tertiary structure,
  49 curvature, and other biophysical attributes of a sequence are currently
  50 not considered.  Polypeptide migration is currently not supported.
  51
  52 =head1 FEEDBACK
  53
  54 =head2 Mailing Lists
  55
  56 User feedback is an integral part of the evolution of this and other
  57 Bioperl modules. Send your comments and suggestions preferably to
  58 the Bioperl mailing list.  Your participation is much appreciated.
  59
  60   bioperl-l@bioperl.org                  - General discussion
  61   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  62
  63 =head2 Support
  64
  65 Please direct usage questions or support issues to the mailing list:
  66
  67 I<bioperl-l@bioperl.org>
  68
  69 rather than to the module maintainer directly. Many experienced and
  70 reponsive experts will be able look at the problem and quickly
  71 address it. Please include a thorough description of the problem
  72 with code and data examples if at all possible.
  73
  74 =head2 Reporting Bugs
  75
  76 Report bugs to the Bioperl bug tracking system to help us keep track
  77 of the bugs and their resolution. Bug reports can be submitted via the
  78 web:
  79
  80   https://github.com/bioperl/bioperl-live/issues
  81
  82 =head1 AUTHOR - Allen Day
  83
  84 Email allenday@ucla.edu
  85
  86 =head1 APPENDIX
  87
  88 The rest of the documentation details each of the object methods.
  89 Internal methods are usually preceded with a _
  90
  91 =cut
  92
  93
  94 package Bio::Tools::Gel;
  95 use strict;
  96
  97 use Bio::PrimarySeq;
  98
  99 use base qw(Bio::Root::Root);
 100
 101 =head2 new
 102
 103  Title   : new
 104  Usage   : my $gel = Bio::Tools::Gel->new(-seq => $sequence,-dilate => 3);
 105  Function: Initializes a new Gel
 106  Returns : Bio::Tools::Gel
 107  Args    : -seq      => Bio::Seq(s), scalar(s) or list of either/both
 108                         (default: none)
 109            -dilate   => Expand band migration distances (default: 1)
 110
 111 =cut
 112
 113 sub new {
 114     my ($class, @args) = @_;
 115
 116     my $self = $class->SUPER::new(@args);
 117     my ($seqs, $dilate) = $self->_rearrange([qw(SEQ DILATE)], @args);
 118     if( ! ref($seqs)  ) {
 119         $self->add_band([$seqs]);
 120     } elsif( ref($seqs) =~ /array/i ||
 121         $seqs->isa('Bio::PrimarySeqI') ) {
 122         $self->add_band($seqs);
 123     }
 124     $self->dilate($dilate || 1);
 125
 126     return $self;
 127 }
 128
 129
 130 =head2 add_band
 131
 132  Title   : add_band
 133  Usage   : $gel->add_band($seq);
 134  Function: Calls _add_band with a (possibly created) Bio::Seq object.
 135  Returns :
 136  Args    : Bio::Seq, scalar sequence, or list of either/both.
 137
 138 =cut
 139
 140 sub add_band {
 141     my ($self, $args) = @_;
 142
 143     foreach my $arg (@$args){
 144         my $seq;
 145         if( ! ref $arg ) {
 146             if( $arg =~ /^\d+/ ) {
 147                 # $arg is a number
 148                 $seq = Bio::PrimarySeq->new(-seq=>'N'x$arg, -id => $arg);
 149             } else {
 150                 # $arg is a sequence string
 151                 $seq = Bio::PrimarySeq->new(-seq=>$arg, -id=>length $arg);
 152             }
 153         } elsif( $arg->isa('Bio::PrimarySeqI') ) {
 154             # $arg is a sequence object
 155             $seq = $arg;
 156         }
 157
 158         $self->_add_band($seq);
 159     }
 160     return 1;
 161 }
 162
 163
 164 =head2 _add_band
 165
 166  Title   : _add_band
 167  Usage   : $gel->_add_band($seq);
 168  Function: Adds a new band to the gel.
 169  Returns :
 170  Args    : Bio::Seq object
 171
 172 =cut
 173
 174 sub _add_band {
 175     my ($self, $arg) = @_;
 176     if ( defined $arg) {
 177         push (@{$self->{'bands'}},$arg);
 178     }
 179     return 1;
 180 }
 181
 182
 183 =head2 dilate
 184
 185  Title   : dilate
 186  Usage   : $gel->dilate(1);
 187  Function: Sets/retrieves the dilation factor.
 188  Returns : dilation factor
 189  Args    : Float or none
 190
 191 =cut
 192
 193 sub dilate {
 194     my ($self, $arg) = @_;
 195     return $self->{dilate} unless $arg;
 196     $self->throw("-dilate should be numeric") if defined $arg and $arg =~ /[^e\d\.]/;
 197     $self->{dilate} = $arg;
 198     return $self->{dilate};
 199 }
 200
 201
 202 sub migrate {
 203     my ($self, $arg) = @_;
 204     $arg = $self unless $arg;
 205     if ( $arg ) {
 206         return 4 - log10($arg);
 207     } else {
 208         return 0;
 209     }
 210 }
 211
 212
 213 =head2 bands
 214
 215  Title   : bands
 216  Usage   : $gel->bands;
 217  Function: Calculates migration distances of sequences.
 218  Returns : hash of (seq_id => distance)
 219  Args    :
 220
 221 =cut
 222
 223 sub bands {
 224     my $self = shift;
 225     $self->throw("bands() is read-only") if @_;
 226
 227     my %bands = ();
 228
 229     foreach my $band (@{$self->{bands}}){
 230         my $distance = $self->dilate * migrate($band->length);
 231         $bands{$band->id} = $distance;
 232     }
 233
 234     return %bands;
 235 }
 236
 237
 238 =head2 log10
 239
 240  Title   : log10
 241  Usage   : log10($n);
 242  Function: returns base 10 log of $n.
 243  Returns : float
 244  Args    : float
 245
 246 =cut
 247
 248 # from "Programming Perl"
 249 sub log10 {
 250     my $n = shift;
 251     return log($n)/log(10);
 252 }
 253
 254 1;