Bio/Tools/Spidey/Exon.pm

   1 #
   2 # BioPerl module for Bio::Tools::Spidey::Exon
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Ryan Golhar <golharam@umdnj.edu>
   7 #
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Tools::Spidey::Exon - A single exon determined by an alignment
  16
  17 =head1 SYNOPSIS
  18
  19   # See Bio::Tools::Spidey::Results for a description of the context.
  20
  21   # an instance of this class is-a Bio::SeqFeature::SimilarityPair
  22
  23   # coordinates of the exon (recommended way):
  24   print "exon from ", $exon->start(),
  25         " to ", $exon->end(), "\n";
  26
  27   # the same (feature1() inherited from Bio::SeqFeature::FeaturePair)
  28   print "exon from ", $exon->feature1()->start(),
  29         " to ", $exon->feature1()->end(), "\n";
  30   # also the same (query() inherited from Bio::SeqFeature::SimilarityPair):
  31   print "exon from ", $exon->query()->start(),
  32         " to ", $exon->query()->end(), "\n";
  33
  34   # coordinates on the matching EST (recommended way):
  35   print "matches on EST from ", $exon->est_hit()->start(),
  36         " to ", $exon->est_hit()->end(), "\n";
  37
  38   # the same (feature2() inherited from Bio::SeqFeature::FeaturePair)
  39   print "matches on EST from ", $exon->feature2()->start(),
  40         " to ", $exon->feature2()->end(), "\n";
  41   # also the same (subject() inherited from Bio::SeqFeature::SimilarityPair):
  42   print "exon from ", $exon->subject()->start(),
  43         " to ", $exon->subject()->end(), "\n";
  44
  45 =head1 DESCRIPTION
  46
  47 This class inherits from Bio::SeqFeature::SimilarityPair and represents an
  48 exon on a genomic sequence determined by similarity, that is, by aligning an
  49 EST sequence (using Spidey in this case). Consequently, the notion of query and
  50 subject is always from the perspective of the genomic sequence: query refers
  51 to the genomic seq, subject to the aligned EST hit. Because of this,
  52 $exon-E<gt>start(), $exon-E<gt>end() etc will always return what you expect.
  53
  54 To get the coordinates on the matching EST, refer to the properties of the
  55 feature returned by L<est_hit>().
  56
  57 =head1 FEEDBACK
  58
  59 =head2 Mailing Lists
  60
  61 User feedback is an integral part of the evolution of this
  62 and other Bioperl modules. Send your comments and suggestions preferably
  63  to one of the Bioperl mailing lists.
  64 Your participation is much appreciated.
  65
  66   bioperl-l@bioperl.org                  - General discussion
  67   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  68
  69 =head2 Support
  70
  71 Please direct usage questions or support issues to the mailing list:
  72
  73 I<bioperl-l@bioperl.org>
  74
  75 rather than to the module maintainer directly. Many experienced and
  76 reponsive experts will be able look at the problem and quickly
  77 address it. Please include a thorough description of the problem
  78 with code and data examples if at all possible.
  79
  80 =head2 Reporting Bugs
  81
  82 Report bugs to the Bioperl bug tracking system to help us keep track
  83 the bugs and their resolution. Bug reports can be submitted via the
  84 web:
  85
  86   https://github.com/bioperl/bioperl-live/issues
  87
  88 =head1 AUTHOR - Ryan Golhar
  89
  90 Email golharam@umdnj.edu
  91
  92 =head1 APPENDIX
  93
  94 The rest of the documentation details each of the object methods.
  95 Internal methods are usually preceded with a _
  96
  97 =cut
  98
  99
 100 # Let the code begin...
 101
 102
 103 package Bio::Tools::Spidey::Exon;
 104 use strict;
 105
 106
 107 use base qw(Bio::SeqFeature::SimilarityPair);
 108
 109 sub new {
 110     my ($class,@args) = @_;
 111     my %param = @args;
 112     my $self = $class->SUPER::new(@args);
 113
 114     my ($prim, $prim_tag, $source, $source_tag) =
 115         $self->_rearrange([qw(PRIMARY
 116                               PRIMARY_TAG
 117                               SOURCE
 118                               SOURCE_TAG)],
 119                           @args);
 120
 121     $self->primary_tag('exon') unless $prim || $prim_tag;
 122     $self->source_tag('Spidey') unless $source || $source_tag;
 123     $self->strand(0) unless defined($self->strand());
 124     $self->query();
 125     return $self;
 126 }
 127
 128 =head2 percentage_id
 129
 130  Title   : percentage_id
 131  Usage   : $obj->percentage_id
 132  Function: This is the percent id as reported by Spidey
 133  Returns : value of percentage_id
 134  Args    :
 135
 136
 137 =cut
 138
 139 sub percentage_id {
 140         my ($self, @args) = @_;
 141         my $val;
 142
 143         if(@args) {
 144             $val = shift(@args);
 145             $self->{'percentage_id'} = $val;
 146         } else {
 147             $val = $self->{'percentage_id'};
 148         }
 149         return $val;
 150 }
 151
 152 =head2 est_hit
 153
 154  Title   : est_hit
 155  Usage   : $est_feature = $obj->est_hit();
 156  Function: Returns the EST hit pointing to (i.e., aligned to by Spidey) this
 157            exon (i.e., genomic region). At present, merely a synonym for
 158            $obj->feature2().
 159  Returns : An Bio::SeqFeatureI implementing object.
 160  Args    :
 161
 162
 163 =cut
 164
 165 sub est_hit {
 166     my $self = shift;
 167     return $self->feature2(@_);
 168 }
 169
 170 =head2 mismatches
 171
 172  Title   : mismatches
 173  Usage   : $obj->mismatches;
 174  Function: Returns the mismatches of the cDNA to (i.e., aligned to by Spidey) this
 175            exon (i.e., genomic region).
 176  Returns : value of mismatches.
 177  Args    :
 178
 179
 180 =cut
 181
 182 sub mismatches {
 183         my ($self, @args) = @_;
 184         my $val;
 185
 186         if(@args) {
 187             $val = shift(@args);
 188             $self->{'mismatches'} = $val;
 189         } else {
 190             $val = $self->{'mismatches'};
 191         }
 192         return $val;
 193 }
 194
 195 =head2 gaps
 196
 197  Title   : gaps
 198  Usage   : $obj->gaps;
 199  Function: Returns the gaps of the cDNA to (i.e., aligned to by Spidey) this
 200            exon (i.e., genomic region).
 201  Returns : value of gaps.
 202  Args    :
 203
 204
 205 =cut
 206
 207 sub gaps {
 208         my ($self, @args) = @_;
 209         my $val;
 210
 211         if(@args) {
 212             $val = shift(@args);
 213             $self->{'gaps'} = $val;
 214         } else {
 215             $val = $self->{'gaps'};
 216         }
 217         return $val;
 218 }
 219
 220 =head2 donor
 221
 222  Title   : donor
 223  Usage   : $obj->donor;
 224  Function: Returns 0 if a splice donor site does not exist, or
 225            1 if a splice donor site exists
 226  Returns : value of existence of donor splice site (0 or 1)
 227  Args    :
 228
 229
 230 =cut
 231
 232 sub donor {
 233         my ($self, @args) = @_;
 234         my $val;
 235
 236         if (@args) {
 237                 $val = shift @args;
 238                 $self->{'donor'} = $val;
 239         } else {
 240                 $val = $self->{'donor'};
 241         }
 242         return $val;
 243 }
 244
 245 =head2 acceptor
 246
 247  Title   : acceptor
 248  Usage   : $obj->acceptor;
 249  Function: Returns 0 if a splice acceptor site does not exist, or
 250            1 if a splice acceptor site exists
 251  Returns : value of existence of acceptor splice site (0 or 1)
 252  Args    :
 253
 254
 255 =cut
 256
 257 sub acceptor {
 258         my ($self, @args) = @_;
 259         my $val;
 260
 261         if (@args) {
 262                 $val = shift @args;
 263                 $self->{'acceptor'} = $val;
 264         } else {
 265                 $val = $self->{'acceptor'};
 266         }
 267         return $val;
 268 }
 269
 270
 271 1;