Bio/SeqFeature/SiRNA/Oligo.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::SiRNA::Pair
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Donald Jackson, donald.jackson@bms.com
   7 #
   8 # Copyright Donald Jackson
   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::SiRNA::Oligo - Perl object for small inhibitory RNAs.
  17
  18 =head1 SYNOPSIS
  19
  20   use Bio::SeqFeature::SiRNA::Oligo;
  21
  22   my $oligo = Bio::SeqFeature::SiRNA::Oligo->
  23       new( -seq         => 'AUGCCGAUUGCAAGUCAGATT',
  24            -start       => 10,
  25            -end         => 31,
  26            -strand      => -1,
  27            -primary     => 'SiRNA::Oligo',
  28            -source_tag  => 'Bio::Tools::SiRNA',
  29            -tag         => { note => 'A note' }, );
  30
  31   # normally two complementary Oligos are combined in an SiRNA::Pair
  32   # object
  33   $pair->antisense($oligo);
  34
  35
  36 =head1 DESCRIPTION
  37
  38 Object methods for single SiRNA oligos - inherits
  39 L<Bio::SeqFeature::Generic>.  Does B<not> include methods for designing
  40 SiRNAs - see L<Bio::Tools::SiRNA> for that.
  41
  42 =head1 SEE ALSO
  43
  44 L<Bio::Tools::SiRNA>, L<Bio::SeqFeature::SiRNA::Pair>.
  45
  46 =head1 FEEDBACK
  47
  48 =head2 Mailing Lists
  49
  50 User feedback is an integral part of the evolution of this and other
  51 Bioperl modules. Send your comments and suggestions preferably to
  52 the Bioperl mailing list.  Your participation is much appreciated.
  53
  54   bioperl-l@bioperl.org                  - General discussion
  55   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  56
  57 =head2 Support
  58
  59 Please direct usage questions or support issues to the mailing list:
  60
  61 I<bioperl-l@bioperl.org>
  62
  63 rather than to the module maintainer directly. Many experienced and
  64 reponsive experts will be able look at the problem and quickly
  65 address it. Please include a thorough description of the problem
  66 with code and data examples if at all possible.
  67
  68 =head2 Reporting Bugs
  69
  70 Report bugs to the Bioperl bug tracking system to help us keep track
  71 of the bugs and their resolution. Bug reports can be submitted via
  72 the web:
  73
  74   https://github.com/bioperl/bioperl-live/issues
  75
  76 =head1 AUTHOR
  77
  78 Donald Jackson (donald.jackson@bms.com)
  79
  80 =head1 APPENDIX
  81
  82 The rest of the documentation details each of the object methods.
  83 Internal methods are usually preceded with a _
  84
  85 =cut
  86
  87 package Bio::SeqFeature::SiRNA::Oligo;
  88
  89 use strict;
  90 use warnings;
  91
  92 use base qw(Bio::SeqFeature::Generic);
  93
  94 our @ARGNAMES = qw(SEQ START END STRAND PRIMARY SOURCE_TAG SCORE TAG
  95                    SEQ_ID ANNOTATION LOCATION);
  96
  97 =head2 new
  98
  99   Title         : new
 100   Usage         : my $sirna_oligo = Bio::SeqFeature::SiRNA::Oligo->new();
 101   Function      : Create a new SiRNA::Oligo object
 102   Returns       : Bio::Tools::SiRNA object
 103   Args          : -seq            sequence of the RNAi oligo.  Should be in RNA alphabet
 104                                   except for the final TT overhang.
 105                   -start          start position
 106                   -end            end position
 107                   -strand         strand
 108                   -primary        primary tag - defaults to 'SiRNA::Oligo'
 109                   -source         source tag
 110                   -score          score value
 111                   -tag            a reference to a tag/value hash
 112                   -seq_id         the display name of the sequence
 113                   -annotation     the AnnotationCollectionI object
 114                   -location       the LocationI object
 115
 116 Currently passing arguments in gff_string or gff1_string is not
 117 supported.  SiRNA::Oligo objects are typically created by a design
 118 algorithm such as Bio::Tools::SiRNA
 119
 120 =cut
 121
 122 sub new {
 123     my ($proto, @args) = @_;
 124
 125     my $pkg = ref($proto) || $proto;
 126
 127     my (%args);
 128
 129     my $self = $pkg->SUPER::new();
 130
 131     @args{@ARGNAMES} = $self->_rearrange(\@ARGNAMES, @args);
 132     # default primary tag
 133     $args{'PRIMARY'} ||= 'SiRNA::Oligo';
 134
 135     $args{'PRIMARY'}            && $self->primary_tag($args{'PRIMARY'});
 136     $args{'SOURCE_TAG'}         && $self->source_tag($args{'SOURCE_TAG'});
 137     $args{'SEQNAME'}            && $self->seqname($args{'SEQNAME'});
 138     $args{'SEQ'}                && $self->seq($args{'SEQ'});
 139     $args{'ANNOTATION'}         && $self->annotation($args{'ANNOTATION'});
 140     $args{'LOCATION'}           && $self->location($args{'LOCATION'});
 141     defined($args{'START'})     && $self->start($args{'START'});
 142     defined($args{'END'})       && $self->end($args{'END'});
 143     defined($args{'STRAND'})    && $self->strand($args{'STRAND'});
 144     defined($args{'SCORE'})     && $self->score($args{'SCORE'});
 145
 146     if ($args{'TAG'}) {
 147         foreach my $t ( keys %{ $args{'TAG'} } ) {
 148             $self->add_tag_value($t, $args{'TAG'}->{$t});
 149         }
 150     }
 151
 152     return $self;
 153 }
 154
 155 =head2 seq
 156
 157   Title         : Seq
 158   Usage         : my $oligo_sequence = $sirna_oligo->seq();
 159   Purpose       : Get/set the sequence of the RNAi oligo
 160   Returns       : Sequence for the RNAi oligo
 161   Args          : Sequence of the RNAi oligo (optional)
 162   Note          : Overloads Bio::SeqFeature::Generic seq method - the oligo and
 163                   parent sequences are different.
 164                   Note that all but the last 2 nucleotides are RNA (per Tuschl and colleagues).
 165                   SiRNA::Pair objects are typically created by a design algorithm such as
 166                   Bio::Tools::SiRNA.
 167
 168 =cut
 169
 170 sub seq {
 171     my ($self, $seq) = @_;
 172     if ($seq) {
 173         # check alphabet
 174         if ($seq =~ /[^ACGTUacgtu]/ ) {
 175             warn "Sequence contains illegal characters";
 176             return;
 177         }
 178         else {
 179             $self->{'seq'} = $seq;
 180         }
 181     }
 182     return $self->{'seq'};
 183 }
 184
 185 1;