lib/Bio/SeqFeature/Tools/FeatureNamer.pm

   1 #
   2 # bioperl module for Bio::SeqFeature::Tools::FeatureNamer
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Chris Mungall <cjm@fruitfly.org>
   7 #
   8 # Copyright Chris Mungall
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features
  17
  18 =head1 SYNOPSIS
  19
  20   use Bio::SeqIO;
  21   use Bio::SeqFeature::Tools::FeatureNamer;
  22
  23   # first fetch a genbank SeqI object
  24   $seqio =
  25     Bio::SeqIO->new(-file=>'AE003644.gbk',
  26                     -format=>'GenBank');
  27   $seq = $seqio->next_seq();
  28
  29   $namer = Bio::SeqFeature::Tools::FeatureNamer->new;
  30   my @features = $seq->get_SeqFeatures;
  31   foreach my $feature (@features) {
  32     $namer->name_feature($feature) unless $feature->display_name;
  33   }
  34
  35 =head1 DESCRIPTION
  36
  37 This is a helper class for providing names for SeqFeatures
  38
  39 The L<Bio::SeqFeatureI> class provides a display_name
  40 method. Typically the display_name is not set when parsing formats
  41 such as genbank - instead properties such as B<label>, B<product> or
  42 B<gene> are set in a somewhat inconsistent manner.
  43
  44 In addition, when generating subfeatures (for example, exons that are
  45 subfeatures of a transcript feature), it is often desirable to name
  46 these subfeatures before either exporting to another format or
  47 reporting to the user.
  48
  49 This module is intended to help given uniform display_names to
  50 features and their subfeatures.
  51
  52 =head1 TODO
  53
  54 Currently the naming policy is hardcoded. It may be desirable to allow
  55 plugging in variations on naming policies; this could be done either
  56 by subclassing, anonymous subroutines (closures) or
  57 parameterization. Contact the author if you feel you have need for a
  58 different naming policy
  59
  60
  61 =head1 FEEDBACK
  62
  63 =head2 Mailing Lists
  64
  65 User feedback is an integral part of the evolution of this and other
  66 Bioperl modules. Send your comments and suggestions preferably to the
  67 Bioperl mailing lists  Your participation is much appreciated.
  68
  69   bioperl-l@bioperl.org                  - General discussion
  70   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  71
  72 =head2 Support
  73
  74 Please direct usage questions or support issues to the mailing list:
  75
  76 I<bioperl-l@bioperl.org>
  77
  78 rather than to the module maintainer directly. Many experienced and
  79 reponsive experts will be able look at the problem and quickly
  80 address it. Please include a thorough description of the problem
  81 with code and data examples if at all possible.
  82
  83 =head2 Reporting Bugs
  84
  85 report bugs to the Bioperl bug tracking system to help us keep track
  86 the bugs and their resolution.  Bug reports can be submitted via the
  87 web:
  88
  89   https://github.com/bioperl/bioperl-live/issues
  90
  91 =head1 AUTHOR - Chris Mungall
  92
  93 Email:  cjm AT fruitfly DOT org
  94
  95 =head1 APPENDIX
  96
  97 The rest of the documentation details each of the object
  98 methods. Internal methods are usually preceded with a _
  99
 100 =cut
 101
 102
 103 # Let the code begin...
 104
 105 package Bio::SeqFeature::Tools::FeatureNamer;
 106 use strict;
 107
 108 # Object preamble - inherits from Bio::Root::Root
 109
 110 use base qw(Bio::Root::Root);
 111
 112 =head2 new
 113
 114  Title   : new
 115  Usage   : $unflattener = Bio::SeqFeature::Tools::FeatureNamer->new();
 116  Function: constructor
 117  Example :
 118  Returns : a new Bio::SeqFeature::Tools::FeatureNamer
 119  Args    : see below
 120
 121
 122 =cut
 123
 124 sub new {
 125     my($class,@args) = @_;
 126     my $self = $class->SUPER::new(@args);
 127
 128 #    my($typemap) =
 129 #       $self->_rearrange([qw(TYPEMAP
 130 #                            )],
 131 #                          @args);#
 132
 133 #    $typemap  && $self->typemap($typemap);
 134     return $self; # success - we hope!
 135 }
 136
 137 =head2 name_feature
 138
 139  Title   : name_feature
 140  Usage   : $namer->name_feature($sf);
 141  Function: sets display_name
 142  Example :
 143  Returns :
 144  Args    : L<Bio::SeqFeatureI>
 145
 146 This method calls generate_feature_name() and uses the returned value
 147 to set the display_name of the feature
 148
 149 =cut
 150
 151 sub name_feature {
 152     my ($self, $sf) = @_;
 153     my $name = $self->generate_feature_name($sf);
 154     $sf->display_name($name);
 155 }
 156
 157 =head2 name_contained_features
 158
 159  Title   : name_contained_features
 160  Usage   : $namer->name_contained_features($sf);
 161  Function: sets display_name for all features contained by sf
 162  Example :
 163  Returns :
 164  Args    : L<Bio::SeqFeatureI>
 165
 166 iterates through all subfeatures of a certain feature (using
 167 get_all_SeqFeatures) and names each subfeatures, based on the
 168 generated name for the holder feature
 169
 170 A subfeature is named by concatenating the generated name of the
 171 container feature with the type and a number.
 172
 173 For example, if the containing feature is a gene with display name
 174 B<dpp>, subfeatures will be named dpp-mRNA-1 dpp-mRNA2 dpp-exon1
 175 dpp-exon2 etc
 176
 177 =cut
 178
 179 sub name_contained_features{
 180    my ($self,$sf) = @_;
 181    my $cname = $self->generate_feature_name($sf);
 182    my @subsfs = $sf->get_all_SeqFeatures;
 183    my %num_by_type = ();
 184    foreach my $ssf (@subsfs) {
 185        my $type = $ssf->primary_tag;
 186        my $num = $num_by_type{$type} || 0;
 187        $num++;
 188        $num_by_type{$type} = $num;
 189        $ssf->display_name("$cname-$type-$num");
 190    }
 191    return;
 192 }
 193
 194 =head2 generate_feature_name
 195
 196  Title   : generate_feature_name
 197  Usage   : $name = $namer->generate_feature_name($sf);
 198  Function: derives a sensible human readable name for a $sf
 199  Example :
 200  Returns : str
 201  Args    : L<Bio::SeqFeatureI>
 202
 203 returns a generated name (but does not actually set display_name).
 204
 205 If display_name is already set, the method will return this
 206
 207 Otherwise, the name will depend on the property:
 208
 209 =over
 210
 211 =item label
 212
 213 =item product
 214
 215 =item gene
 216
 217 =item locus_tag
 218
 219 =back
 220
 221 (in order of priority)
 222
 223 =cut
 224
 225 sub generate_feature_name {
 226     my ($self, $sf) = @_;
 227
 228     my $name = $sf->display_name;
 229     if (!$name) {
 230         if ($sf->has_tag("label")) {
 231             ($name) = $sf->get_tag_values("label");
 232         }
 233         elsif ($sf->has_tag("product")) {
 234             ($name) = $sf->get_tag_values("product");
 235         }
 236         elsif ($sf->primary_tag eq 'gene' &&
 237                $sf->has_tag("gene")) {
 238             ($name) = $sf->get_tag_values("gene");
 239         }
 240         elsif ($sf->primary_tag eq 'gene' &&
 241                $sf->has_tag("locus_tag")) {
 242             ($name) = $sf->get_tag_values("locus_tag");
 243         }
 244         else {
 245             $name =  $sf->display_name;
 246         }
 247     }
 248     return $name;
 249 }
 250
 251 1;