lib/Bio/Tools/Sim4/Exon.pm

   1 #
   2 # BioPerl module for Bio::Tools::Sim4::Exon
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Ewan Birney <birney-at-sanger.ac.uk>
   7 # and Hilmar Lapp <hlapp-at-gmx.net>
   8 #
   9 # Copyright Ewan Birney, Hilmar Lapp
  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::Tools::Sim4::Exon - A single exon determined by an alignment
  18
  19 =head1 SYNOPSIS
  20
  21   # See Bio::Tools::Sim4::Results for a description of the context.
  22
  23   # an instance of this class is-a Bio::SeqFeature::SimilarityPair
  24
  25   # coordinates of the exon (recommended way):
  26   print "exon from ", $exon->start(),
  27         " to ", $exon->end(), "\n";
  28
  29   # the same (feature1() inherited from Bio::SeqFeature::FeaturePair)
  30   print "exon from ", $exon->feature1()->start(),
  31         " to ", $exon->feature1()->end(), "\n";
  32   # also the same (query() inherited from Bio::SeqFeature::SimilarityPair):
  33   print "exon from ", $exon->query()->start(),
  34         " to ", $exon->query()->end(), "\n";
  35
  36   # coordinates on the matching EST (recommended way):
  37   print "matches on EST from ", $exon->est_hit()->start(),
  38         " to ", $exon->est_hit()->end(), "\n";
  39
  40   # the same (feature2() inherited from Bio::SeqFeature::FeaturePair)
  41   print "matches on EST from ", $exon->feature2()->start(),
  42         " to ", $exon->feature2()->end(), "\n";
  43   # also the same (subject() inherited from Bio::SeqFeature::SimilarityPair):
  44   print "exon from ", $exon->subject()->start(),
  45         " to ", $exon->subject()->end(), "\n";
  46
  47 =head1 DESCRIPTION
  48
  49 This class inherits from Bio::SeqFeature::SimilarityPair and represents an
  50 exon on a genomic sequence determined by similarity, that is, by aligning an
  51 EST sequence (using Sim4 in this case). Consequently, the notion of query and
  52 subject is always from the perspective of the genomic sequence: query refers
  53 to the genomic seq, subject to the aligned EST hit. Because of this,
  54 $exon-E<gt>start(), $exon-E<gt>end() etc will always return what you expect.
  55
  56 To get the coordinates on the matching EST, refer to the properties of the
  57 feature returned by L<est_hit>().
  58
  59 =head1 FEEDBACK
  60
  61 =head2 Mailing Lists
  62
  63 User feedback is an integral part of the evolution of this
  64 and other Bioperl modules. Send your comments and suggestions preferably
  65  to one of the Bioperl mailing lists.
  66 Your participation is much appreciated.
  67
  68   bioperl-l@bioperl.org                  - General discussion
  69   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  70
  71 =head2 Support
  72
  73 Please direct usage questions or support issues to the mailing list:
  74
  75 I<bioperl-l@bioperl.org>
  76
  77 rather than to the module maintainer directly. Many experienced and
  78 reponsive experts will be able look at the problem and quickly
  79 address it. Please include a thorough description of the problem
  80 with code and data examples if at all possible.
  81
  82 =head2 Reporting Bugs
  83
  84 Report bugs to the Bioperl bug tracking system to help us keep track
  85 the bugs and their resolution.  Bug reports can be submitted via the
  86 web:
  87
  88   https://github.com/bioperl/bioperl-live/issues
  89
  90 =head1 AUTHOR - Ewan Birney, Hilmar Lapp
  91
  92 Ewan Birney E<lt>birney-at-sanger.ac.ukE<gt>
  93 Hilmar Lapp E<lt>hlapp-at-gmx.netE<gt> or E<lt>hilmar.lapp-at-pharma.novartis.comE<gt>.
  94
  95 =head1 APPENDIX
  96
  97 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
  98
  99 =cut
 100
 101
 102 # Let the code begin...
 103
 104
 105 package Bio::Tools::Sim4::Exon;
 106
 107 use strict;
 108
 109
 110 use base qw(Bio::SeqFeature::SimilarityPair);
 111
 112 sub new {
 113     my ($class,@args) = @_;
 114     my %param = @args;
 115     my $self = $class->SUPER::new(@args);
 116
 117     my ($prim, $prim_tag, $source, $source_tag) =
 118         $self->_rearrange([qw(PRIMARY
 119                               PRIMARY_TAG
 120                               SOURCE
 121                               SOURCE_TAG)],
 122                           @args);
 123
 124     $self->primary_tag('exon') unless $prim || $prim_tag;
 125     $self->source_tag('Sim4') unless $source || $source_tag;
 126     $self->strand(0) unless defined($self->strand());
 127     $self->query();
 128     return $self;
 129 }
 130
 131 =head2 percentage_id
 132
 133  Title   : percentage_id
 134  Usage   : $obj->percentage_id($newval)
 135  Function: This is a synonym for 100 * $obj->est_hit()->frac_identical().
 136  Returns : value of percentage_id
 137  Args    : newvalue (optional)
 138
 139
 140 =cut
 141
 142 sub percentage_id {
 143     my ($self, @args) = @_;
 144     my $frac;
 145     my $val;
 146     my $delegated = 0;
 147
 148     if(@args) {
 149         $frac = $args[0];
 150         $frac /= 100.0 if defined($frac);
 151     }
 152     if($self->query()->can('frac_identical')) {
 153         if(defined($frac)) {
 154             $self->query()->frac_identical($frac);
 155         }
 156         $val = 100.0 * $self->query()->frac_identical();
 157         $delegated = 1;
 158     }
 159     if($self->est_hit()->can('frac_identical')) {
 160         if(defined($frac)) {
 161             $self->est_hit()->frac_identical($frac);
 162         }
 163         # this intentiously overwrites previous $val
 164         $val = 100.0 * $self->est_hit()->frac_identical();
 165         $delegated = 1;
 166     }
 167     if(! $delegated) {
 168         if(@args) {
 169             $val = shift(@args);
 170             $self->{'percentage_id'} = $val;
 171         } else {
 172             $val = $self->{'percentage_id'};
 173         }
 174     }
 175     return $val;
 176 }
 177
 178 =head2 est_hit
 179
 180  Title   : est_hit
 181  Usage   : $est_feature = $obj->est_hit();
 182  Function: Returns the EST hit pointing to (i.e., aligned to by Sim4) this
 183            exon (i.e., genomic region). At present, merely a synonym for
 184            $obj->feature2().
 185  Returns : An Bio::SeqFeatureI implementing object.
 186  Args    :
 187
 188
 189 =cut
 190
 191 sub est_hit {
 192     my $self = shift;
 193     return $self->feature2(@_);
 194 }
 195
 196 1;