lib/Bio/SeqFeature/Gene/Intron.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::Gene::Intron
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by David Block <dblock@gene.pbi.nrc.ca>
   7 #
   8 # Copyright David Block
   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::Gene::Intron - An intron feature
  17
  18 =head1 SYNOPSIS
  19
  20 Give standard usage here
  21
  22 =head1 DESCRIPTION
  23
  24 Describe the object here
  25
  26 =head1 FEEDBACK
  27
  28 =head2 Mailing Lists
  29
  30 User feedback is an integral part of the evolution of this and other
  31 Bioperl modules. Send your comments and suggestions preferably to
  32 the Bioperl mailing list.  Your participation is much appreciated.
  33
  34   bioperl-l@bioperl.org                  - General discussion
  35   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  36
  37 =head2 Support
  38
  39 Please direct usage questions or support issues to the mailing list:
  40
  41 I<bioperl-l@bioperl.org>
  42
  43 rather than to the module maintainer directly. Many experienced and
  44 reponsive experts will be able look at the problem and quickly
  45 address it. Please include a thorough description of the problem
  46 with code and data examples if at all possible.
  47
  48 =head2 Reporting Bugs
  49
  50 Report bugs to the Bioperl bug tracking system to help us keep track
  51 of the bugs and their resolution. Bug reports can be submitted via the
  52 web:
  53
  54   https://github.com/bioperl/bioperl-live/issues
  55
  56 =head1 AUTHOR - David Block
  57
  58 Email dblock@gene.pbi.nrc.ca
  59
  60 =head1 APPENDIX
  61
  62 The rest of the documentation details each of the object methods.
  63 Internal methods are usually preceded with a _
  64
  65 =cut
  66
  67
  68 # Let the code begin...
  69
  70
  71 package Bio::SeqFeature::Gene::Intron;
  72
  73 use strict;
  74
  75 use Bio::SeqFeature::Gene::Exon;
  76
  77 use base qw(Bio::SeqFeature::Gene::NC_Feature);
  78
  79 sub new {
  80     my($class,@args) = @_;
  81
  82     # introns are non-coding by default
  83     if(! grep { lc($_) eq '-is_coding'; } @args) {
  84         push(@args, '-is_coding', 0);
  85     }
  86     my $self = $class->SUPER::new(@args);
  87
  88     my ($primary, $prim) =
  89         $self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args);
  90     $self->primary_tag('intron') unless $primary || $prim;
  91
  92     return $self;
  93 }
  94
  95 =head2 upstream_Exon
  96
  97   Title   : upstream_Exon
  98   Usage   : $intron->upstream_Exon()
  99   Function: exon upstream of the intron
 100   Returns : Bio::EnsEMBL::Exon
 101   Args    :
 102
 103 =cut
 104
 105 sub upstream_Exon {
 106     my( $self, $exon ) = @_;
 107
 108     if ($exon) {
 109         $self->{'_intron_location'} = undef;
 110         $self->throw("'$exon' is not a Bio::SeqFeature::Gene::ExonI")
 111             unless $exon->isa('Bio::SeqFeature::Gene::ExonI');
 112         $self->{'_upstream_exon'} = $exon;
 113     }
 114     return $self->{'_upstream_exon'};
 115 }
 116
 117
 118 =head2 downstream_Exon
 119
 120   Title   : downstream_Exon
 121   Usage   : $intron->downstream_Exon()
 122   Function: exon downstream of the intron
 123   Returns : Bio::EnsEMBL::Exon
 124   Args    :
 125
 126 =cut
 127
 128 sub downstream_Exon {
 129     my( $self, $exon ) = @_;
 130
 131     if ($exon) {
 132         $self->{'_intron_location'} = undef;
 133         $self->throw("'$exon' is not a Bio::SeqFeature::Gene::ExonI")
 134             unless $exon->isa('Bio::SeqFeature::Gene::ExonI');
 135         $self->{'_downstream_exon'} = $exon;
 136     }
 137     return $self->{'_downstream_exon'};
 138 }
 139
 140 =head2 phase
 141
 142   Title   : phase
 143   Usage   : $intron->phase()
 144   Function: returns the phase of the intron(where it interrupts the codon)
 145   Returns : int(0,1,2)
 146   Args    :
 147
 148 =cut
 149
 150 sub phase {
 151   my ($self) = @_;
 152   return $self->downstream_Exon->phase;
 153 }
 154
 155
 156 =head2 acceptor_splice_site
 157
 158   Title   : acceptor_splice_site
 159   Usage   : $intron->acceptor_splice_site(21,3)
 160   Function: returns the sequence corresponding to the
 161             consensus acceptor splice site. If start and
 162             end are provided, it will number of base pairs
 163             left and right of the canonical AG. Here 21 means
 164             21 bp into intron and 3 means 3 bp into the exon.
 165             --Intron--21----|AG|-3-----Exon
 166             Defaults to 21,3
 167
 168   Returns : Bio::Seq
 169   Args    : start and end
 170
 171 =cut
 172
 173 sub acceptor_splice_site {
 174   my ($self,$ss_start,$ss_end) = @_;
 175   $ss_start = 21 unless defined $ss_start;
 176   $ss_end   = 3 unless defined $ss_end;
 177   if($self->strand < 0){
 178     my $tmp= $ss_start;
 179     $ss_start = $ss_end;
 180     $ss_end = $tmp;
 181   }
 182   my $intron_end= $self->location->end;
 183   my $down_exon = $self->downstream_Exon;
 184   my $acceptor;
 185   if($self->strand < 0){
 186       $ss_start= $ss_start >  $down_exon->length ? $down_exon->length: $ss_start;
 187       $ss_end= $ss_end > $self->length-2 ? $self->length-2 : $ss_end;
 188       $acceptor = Bio::SeqFeature::Generic->new(-start=>$self->start - ($ss_start) ,
 189                                                -end=>$self->start + ($ss_end+1),
 190                                                -strand=>$self->strand,
 191                                                -primary_tag=>"donor splice site");
 192   }
 193   else {
 194     $ss_start = $ss_start > $self->length-2 ? $self->length-2 : $ss_start;
 195     $ss_end = $ss_end > $down_exon->length ? $down_exon->length : $ss_end;
 196
 197
 198     $acceptor = Bio::SeqFeature::Generic->new(-start=>$self->end - ($ss_start + 1),
 199                                                -end=>$self->end + $ss_end,
 200                                                -strand=>$self->strand,
 201                                                -primary_tag=>"donor splice site");
 202   }
 203   $acceptor->attach_seq($self->entire_seq);
 204
 205   return $acceptor;
 206
 207 }
 208
 209 =head2 donor_splice_site
 210
 211   Title   : donor_splice_site
 212   Usage   : $intron->donor_splice_site(3,6)
 213   Function: returns the sequence corresponding to the
 214             consensus donor splice site. If start and
 215             end are provided, it will number of base pairs
 216             left and right of the canonical GT. Here 3 means
 217             3 bp into exon and 6 means 6 bp into the intron.
 218             --Exon-3--|GT|-6----Intron-
 219             Defaults to 3,6
 220
 221   Returns : Bio::Seq
 222   Args    : start and end
 223
 224 =cut
 225
 226 sub donor_splice_site {
 227   my ($self,$ss_start,$ss_end) = @_;
 228   $ss_start = 3 unless defined $ss_start;
 229   $ss_end   = 10 unless defined $ss_end;
 230   if($self->strand < 0){
 231     my $tmp= $ss_start;
 232     $ss_start = $ss_end;
 233     $ss_end = $tmp;
 234   }
 235   my $up_exon = $self->upstream_Exon;
 236   my $donor;
 237   if($self->strand < 0){
 238     $ss_end = $ss_end > $up_exon->length ? $up_exon->length : $ss_end;
 239     $ss_start   = $ss_start> $self->length -2 ? $self->length -2 : $ss_start;
 240     $donor = Bio::SeqFeature::Generic->new(-start=>$self->end -  ($ss_start+1),
 241                                             -end  => $self->end + ($ss_end),
 242                                             -strand=>$self->strand,
 243                                             -primary_tag=>"acceptor splice site");
 244   }
 245   else {
 246     $ss_start = $ss_start > $up_exon->length ? $up_exon->length : $ss_start;
 247     $ss_end   = $ss_end > $self->length -2 ? $self->length -2 : $ss_end;
 248     $donor = Bio::SeqFeature::Generic->new(-start=>$self->start - $ss_start,
 249                                            -end  => $self->start +($ss_end+1),
 250                                             -strand=>$self->strand,
 251                                             -primary_tag=>"acceptor splice site");
 252   }
 253   $donor->attach_seq($self->entire_seq);
 254   return $donor;
 255 }
 256
 257 sub location {
 258     my( $self ) = @_;
 259
 260     unless ($self->{'_intron_location'}) {
 261         my $loc = Bio::Location::Simple->new;
 262
 263         my $up_exon = $self->upstream_Exon;
 264         my $down_exon = $self->downstream_Exon;
 265
 266         # Get the PrimarySeqs attached to both and check it is the same sequence
 267         my $up_seq   = $up_exon  ->entire_seq;
 268         my $down_seq = $down_exon->entire_seq;
 269         unless (ref($up_seq) eq ref($down_seq) ) {
 270             $self->throw("upstream and downstream exons are attached to different sequences\n'$up_seq' and '$down_seq'");
 271         }
 272
 273         # Check that the exons are on the same strand.  (Do I need to bother?)
 274         my $up_strand   = $up_exon  ->strand;
 275         my $down_strand = $down_exon->strand;
 276         unless ($up_strand == $down_strand) {
 277             $self->throw("upstream and downstream exons are on different strands "
 278                 . "('$up_strand' and '$down_strand')");
 279         }
 280         $loc->strand($up_strand);
 281
 282         #   $exon_end is the  end  of the exon which is 5' of the intron on the genomic sequence.
 283         # $exon_start is the start of the exon which is 3' of the intron on the genomic sequence.
 284         my( $exon_end, $exon_start );
 285         if ($up_strand == 1) {
 286             $exon_end   = $up_exon  ->end;
 287             $exon_start = $down_exon->start;
 288         } else {
 289             $exon_end   = $down_exon->end;
 290             $exon_start = $up_exon  ->start;
 291         }
 292         unless ($exon_end < $exon_start) {
 293             $self->throw("Intron gap begins after '$exon_end' and ends before '$exon_start'");
 294         }
 295         $loc->start($exon_end   + 1);
 296         $loc->end  ($exon_start - 1);
 297
 298         # Attach the sequence and location objects to the intron
 299         $self->{'_intron_location'} = $loc;
 300
 301     }
 302     return $self->{'_intron_location'};
 303 }
 304 1;