Bio/SearchDist.pm

   1
   2 #
   3 # BioPerl module for Bio::SearchDist
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   8 #
   9 # Copyright Ewan Birney
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object
  18
  19 =head1 SYNOPSIS
  20
  21   $dis = Bio::SearchDist->new();
  22   foreach $score ( @scores ) {
  23      $dis->add_score($score);
  24   }
  25
  26   if( $dis->fit_evd() ) {
  27     foreach $score ( @scores ) {
  28       $evalue = $dis->evalue($score);
  29       print "Score $score had an evalue of $evalue\n";
  30     }
  31   } else {
  32     warn("Could not fit histogram to an EVD!");
  33   }
  34
  35 =head1 DESCRIPTION
  36
  37 The Bio::SearchDist object is a wrapper around Sean Eddy's excellent
  38 histogram object. The histogram object can bascially take in a number
  39 of scores which are sensibly distributed somewhere around 0 that come
  40 from a supposed Extreme Value Distribution. Having add all the scores
  41 from a database search via the add_score method you can then fit a
  42 extreme value distribution using fit_evd(). Once fitted you can then
  43 get out the evalue for each score (or a new score) using
  44 evalue($score).
  45
  46 The fitting procedure is better described in Sean Eddy's own code
  47 (available from http://hmmer.janelia.org/, or in the histogram.h header
  48 file in Compile/SW). Bascially it fits a EVD via a maximum likelhood
  49 method with pruning of the top end of the distribution so that real
  50 positives are discarded in the fitting procedure. This comes from
  51 an orginally idea of Richard Mott's and the likelhood fitting
  52 is from a book by Lawless [should ref here].
  53
  54
  55 The object relies on the fact that the scores are sensibly distributed
  56 around about 0 and that integer bins are sensible for the
  57 histogram. Scores based on bits are often ideal for this (bits based
  58 scoring mechanisms is what this histogram object was originally
  59 designed for).
  60
  61
  62 =head1 CONTACT
  63
  64 The original code this was based on comes from the histogram module as
  65 part of the HMMer2 package. Look at http://hmmer.janelia.org/
  66
  67 Its use in Bioperl is via the Compiled XS extension which is cared for
  68 by Ewan Birney (birney@ebi.ac.uk). Please contact Ewan first about
  69 the use of this module
  70
  71 =head1 FEEDBACK
  72
  73 =head2 Mailing Lists
  74
  75 User feedback is an integral part of the evolution of this and other
  76 Bioperl modules. Send your comments and suggestions preferably to one
  77 of the Bioperl mailing lists.  Your participation is much appreciated.
  78
  79   bioperl-l@bioperl.org                  - General discussion
  80   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  81
  82 =head2 Support
  83
  84 Please direct usage questions or support issues to the mailing list:
  85
  86 I<bioperl-l@bioperl.org>
  87
  88 rather than to the module maintainer directly. Many experienced and
  89 reponsive experts will be able look at the problem and quickly
  90 address it. Please include a thorough description of the problem
  91 with code and data examples if at all possible.
  92
  93 =head2 Reporting Bugs
  94
  95 Report bugs to the Bioperl bug tracking system to help us keep track
  96 the bugs and their resolution.  Bug reports can be submitted via the
  97 web:
  98
  99   https://github.com/bioperl/bioperl-live/issues
 100
 101 =head1 APPENDIX
 102
 103 The rest of the documentation details each of the object
 104 methods. Internal methods are usually preceded with a _
 105
 106 =cut
 107
 108
 109 # Let the code begin...
 110
 111
 112 package Bio::SearchDist;
 113 use strict;
 114
 115
 116 BEGIN {
 117     eval {
 118         require Bio::Ext::Align;
 119     };
 120     if ( $@ ) {
 121 print $@;
 122         print STDERR ("\nThe C-compiled engine for histogram object (Bio::Ext::Align) has not been installed.\n Please install the bioperl-ext package\n\n");
 123         exit(1);
 124     }
 125 }
 126
 127
 128 use base qw(Bio::Root::Root);
 129
 130 sub new {
 131   my($class,@args) = @_;
 132   my $self = $class->SUPER::new(@args);
 133   my($min, $max, $lump) =
 134         $self->_rearrange([qw(MIN MAX LUMP)], @args);
 135
 136   if( !  $min ) {
 137     $min = -100;
 138   }
 139
 140   if( !  $max ) {
 141     $max = +100;
 142   }
 143
 144   if( ! $lump ) {
 145     $lump = 50;
 146   }
 147
 148   $self->_engine(&Bio::Ext::Align::new_Histogram($min,$max,$lump));
 149
 150   return $self;
 151 }
 152
 153 =head2 add_score
 154
 155  Title   : add_score
 156  Usage   : $dis->add_score(300);
 157  Function: Adds a single score to the distribution
 158  Returns : nothing
 159  Args    :
 160
 161
 162 =cut
 163
 164 sub add_score{
 165    my ($self,$score) = @_;
 166    my ($eng);
 167    $eng = $self->_engine();
 168    #$eng->AddToHistogram($score);
 169    $eng->add($score);
 170 }
 171
 172 =head2 fit_evd
 173
 174  Title   : fit_evd
 175  Usage   : $dis->fit_evd();
 176  Function: fits an evd to the current distribution
 177  Returns : 1 if it fits successfully, 0 if not
 178  Args    :
 179
 180
 181 =cut
 182
 183 sub fit_evd{
 184    my ($self,@args) = @_;
 185
 186    return $self->_engine()->fit_EVD(10000,1);
 187 }
 188
 189 =head2 fit_Gaussian
 190
 191  Title   : fit_Gaussian
 192  Usage   :
 193  Function:
 194  Example :
 195  Returns :
 196  Args    :
 197
 198
 199 =cut
 200
 201 sub fit_Gaussian{
 202    my ($self,$high) = @_;
 203
 204    if( ! defined $high ) {
 205        $high = 10000;
 206    }
 207
 208    return $self->_engine()->fit_Gaussian($high);
 209 }
 210
 211
 212 =head2 evalue
 213
 214  Title   : evalue
 215  Usage   : $eval = $dis->evalue($score)
 216  Function: Returns the evalue of this score
 217  Returns : float
 218  Args    :
 219
 220
 221 =cut
 222
 223 sub evalue{
 224    my ($self,$score) = @_;
 225
 226    return $self->_engine()->evalue($score);
 227
 228 }
 229
 230
 231
 232 =head2 _engine
 233
 234  Title   : _engine
 235  Usage   : $obj->_engine($newval)
 236  Function: underlyine bp_sw:: histogram engine
 237  Returns : value of _engine
 238  Args    : newvalue (optional)
 239
 240
 241 =cut
 242
 243 sub _engine{
 244     my ($self,$value) = @_;
 245     if( defined $value) {
 246         $self->{'_engine'} = $value;
 247     }
 248     return $self->{'_engine'};
 249 }
 250
 251
 252 ## End of Package
 253
 254 1;
 255 __END__
 256