lib/Bio/SeqFeature/Gene/TranscriptI.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::Gene::TranscriptI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   7 #
   8 # Copyright Hilmar Lapp
   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::TranscriptI - Interface for a feature representing a
  17          transcript of exons, promoter(s), UTR, and a poly-adenylation site.
  18
  19 =head1 SYNOPSIS
  20
  21   #documentation needed
  22
  23 =head1 DESCRIPTION
  24
  25 A feature representing a transcript.
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this
  32 and other Bioperl modules. Send your comments and suggestions preferably
  33  to one of the Bioperl mailing lists.
  34 Your participation is much appreciated.
  35
  36   bioperl-l@bioperl.org                  - General discussion
  37   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  38
  39 =head2 Support
  40
  41 Please direct usage questions or support issues to the mailing list:
  42
  43 I<bioperl-l@bioperl.org>
  44
  45 rather than to the module maintainer directly. Many experienced and
  46 reponsive experts will be able look at the problem and quickly
  47 address it. Please include a thorough description of the problem
  48 with code and data examples if at all possible.
  49
  50 =head2 Reporting Bugs
  51
  52 Report bugs to the Bioperl bug tracking system to help us keep track
  53 the bugs and their resolution.  Bug reports can be submitted via the
  54 web:
  55
  56   https://github.com/bioperl/bioperl-live/issues
  57
  58 =head1 AUTHOR - Hilmar Lapp
  59
  60 Email hlapp@gmx.net
  61
  62 =head1 APPENDIX
  63
  64 The rest of the documentation details each of the object methods.
  65 Internal methods are usually preceded with a _
  66
  67 =cut
  68
  69
  70 # Let the code begin...
  71
  72
  73 package Bio::SeqFeature::Gene::TranscriptI;
  74 use strict;
  75
  76 use Carp;
  77
  78 use base qw(Bio::SeqFeatureI);
  79
  80 =head2 promoters
  81
  82  Title   : promoters()
  83  Usage   : @proms = $transcript->promoters();
  84  Function: Get the promoter features of this transcript.
  85
  86            Note that OO-modeling of regulatory elements is not stable yet.
  87            This means that this method might change or even disappear in a
  88            future release. Be aware of this if you use it.
  89
  90  Returns : An array of Bio::SeqFeatureI implementing objects representing the
  91            promoter regions or sites.
  92  Args    :
  93
  94 =cut
  95
  96 sub promoters {
  97     my ($self) = @_;
  98     $self->throw_not_implemented();
  99 }
 100
 101 =head2 exons
 102
 103  Title   : exons()
 104  Usage   : @exons = $transcript->exons();
 105            @inital = $transcript->exons('Initial');
 106  Function: Get the individual exons this transcript comprises of, or all exons
 107            of a specified type.
 108
 109            Refer to the documentation of the class that produced this
 110            transcript object for information about the possible types.
 111
 112            See Bio::SeqFeature::Gene::ExonI for properties of the
 113            returned objects.
 114
 115  Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
 116  Args    : An optional string specifying the type of the exon.
 117
 118 =cut
 119
 120 sub exons {
 121     my ($self, $type) = @_;
 122     $self->throw_not_implemented();
 123 }
 124
 125 =head2 introns
 126
 127  Title   : introns()
 128  Usage   : @introns = $transcript->introns();
 129  Function: Get all introns this transcript comprises of.
 130  Returns : An array of Bio::SeqFeatureI implementing objects representing the
 131            introns.
 132  Args    :
 133
 134
 135 =cut
 136
 137 sub introns {
 138     my ($self) = @_;
 139     $self->throw_not_implemented();
 140 }
 141
 142 =head2 poly_A_site
 143
 144  Title   : poly_A_site()
 145  Usage   : $polyAsite = $transcript->poly_A_site();
 146  Function: Get the poly-adenylation site of this transcript.
 147  Returns : A Bio::SeqFeatureI implementing object.
 148  Args    :
 149
 150
 151 =cut
 152
 153 sub poly_A_site {
 154     my ($self) = @_;
 155     $self->throw_not_implemented();
 156 }
 157
 158 =head2 utrs
 159
 160  Title   : utrs()
 161  Usage   : @utr_sites = $transcript->utrs();
 162  Function: Get the UTR regions this transcript comprises of.
 163
 164            See Bio::SeqFeature::Gene::ExonI for properties of the
 165            returned objects.
 166
 167  Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
 168  Args    :
 169
 170
 171 =cut
 172
 173 sub utrs {
 174     my ($self) = @_;
 175     $self->throw_not_implemented();
 176 }
 177
 178 =head2 mrna
 179
 180  Title   : mrna()
 181  Usage   : $mrna = $transcript->mrna();
 182  Function: Get the mRNA of the transcript as a sequence object.
 183
 184  Returns : A Bio::PrimarySeqI implementing object.
 185  Args    :
 186
 187
 188 =cut
 189
 190 sub mrna {
 191     my ($self) = @_;
 192     $self->throw_not_implemented();
 193 }
 194
 195 =head2 cds
 196
 197  Title   : cds()
 198  Usage   : $cds = $transcript->cds();
 199  Function: Get the CDS (coding sequence) of the transcript as a sequence
 200            object.
 201
 202  Returns : A Bio::PrimarySeqI implementing object.
 203  Args    :
 204
 205
 206 =cut
 207
 208 sub cds {
 209     my ($self) = @_;
 210     $self->throw_not_implemented();
 211 }
 212
 213 =head2 protein
 214
 215  Title   : protein()
 216  Usage   : $protein = $transcript->protein();
 217  Function: Get the protein encoded by the transcript as a sequence object.
 218
 219  Returns : A Bio::PrimarySeqI implementing object.
 220  Args    :
 221
 222
 223 =cut
 224
 225 sub protein {
 226     my ($self) = @_;
 227     $self->throw_not_implemented();
 228 }
 229
 230 =head2 parent
 231
 232  Title   : parent
 233  Usage   : $obj->parent($newval)
 234  Function: get the parent gene of the transcript
 235  Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object
 236  Args    : a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)
 237
 238
 239 =cut
 240
 241 sub parent{
 242    my $self = shift;
 243    if( @_ ) {
 244        my $value = shift;
 245        # I really mean ! defined $value -
 246        # we will allow re-setting the parent to undef
 247        if (! defined $value ||
 248            $value->isa("Bio::SeqFeature::Gene::GeneStructureI")) {
 249            $self->{'_parent'} = $value;
 250        } else {
 251            $self->throw("$value must be a Bio::SeqFeature::Gene::GeneStructureI")
 252        }
 253     }
 254     return $self->{'_parent'};
 255 }
 256
 257
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