#
# BioPerl module for Bio::SeqFeature::SiRNA::Pair
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Donald Jackson, donald.jackson@bms.com
#
# Copyright Donald Jackson
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.
=head1 SYNOPSIS
use Bio::SeqFeature::SiRNA::Oligo;
my $oligo = Bio::SeqFeature::SiRNA::Oligo->
new( -seq => 'AUGCCGAUUGCAAGUCAGATT',
-start => 10,
-end => 31,
-strand => -1,
-primary => 'SiRNA::Oligo',
-source_tag => 'Bio::Tools::SiRNA',
-tag => { note => 'A note' }, );
# normally two complementary Oligos are combined in an SiRNA::Pair
# object
$pair->antisense($oligo);
=head1 DESCRIPTION
Object methods for single SiRNA oligos - inherits
L<Bio::SeqFeature::Generic>. Does B<not> include methods for designing
SiRNAs - see L<Bio::Tools::SiRNA> for that.
=head1 SEE ALSO
L<Bio::Tools::SiRNA>, L<Bio::SeqFeature::SiRNA::Pair>.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Donald Jackson (donald.jackson@bms.com)
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::SeqFeature::SiRNA::Oligo;
use strict;
use warnings;
use base qw(Bio::SeqFeature::Generic);
our @ARGNAMES = qw(SEQ START END STRAND PRIMARY SOURCE_TAG SCORE TAG
SEQ_ID ANNOTATION LOCATION);
=head2 new
Title : new
Usage : my $sirna_oligo = Bio::SeqFeature::SiRNA::Oligo->new();
Function : Create a new SiRNA::Oligo object
Returns : Bio::Tools::SiRNA object
Args : -seq sequence of the RNAi oligo. Should be in RNA alphabet
except for the final TT overhang.
-start start position
-end end position
-strand strand
-primary primary tag - defaults to 'SiRNA::Oligo'
-source source tag
-score score value
-tag a reference to a tag/value hash
-seq_id the display name of the sequence
-annotation the AnnotationCollectionI object
-location the LocationI object
Currently passing arguments in gff_string or gff1_string is not
supported. SiRNA::Oligo objects are typically created by a design
algorithm such as Bio::Tools::SiRNA
=cut
sub new {
my ($proto, @args) = @_;
my $pkg = ref($proto) || $proto;
my (%args);
my $self = $pkg->SUPER::new();
@args{@ARGNAMES} = $self->_rearrange(\@ARGNAMES, @args);
# default primary tag
$args{'PRIMARY'} ||= 'SiRNA::Oligo';
$args{'PRIMARY'} && $self->primary_tag($args{'PRIMARY'});
$args{'SOURCE_TAG'} && $self->source_tag($args{'SOURCE_TAG'});
$args{'SEQNAME'} && $self->seqname($args{'SEQNAME'});
$args{'SEQ'} && $self->seq($args{'SEQ'});
$args{'ANNOTATION'} && $self->annotation($args{'ANNOTATION'});
$args{'LOCATION'} && $self->location($args{'LOCATION'});
defined($args{'START'}) && $self->start($args{'START'});
defined($args{'END'}) && $self->end($args{'END'});
defined($args{'STRAND'}) && $self->strand($args{'STRAND'});
defined($args{'SCORE'}) && $self->score($args{'SCORE'});
if ($args{'TAG'}) {
foreach my $t ( keys %{ $args{'TAG'} } ) {
$self->add_tag_value($t, $args{'TAG'}->{$t});
}
}
return $self;
}
=head2 seq
Title : Seq
Usage : my $oligo_sequence = $sirna_oligo->seq();
Purpose : Get/set the sequence of the RNAi oligo
Returns : Sequence for the RNAi oligo
Args : Sequence of the RNAi oligo (optional)
Note : Overloads Bio::SeqFeature::Generic seq method - the oligo and
parent sequences are different.
Note that all but the last 2 nucleotides are RNA (per Tuschl and colleagues).
SiRNA::Pair objects are typically created by a design algorithm such as
Bio::Tools::SiRNA.
=cut
sub seq {
my ($self, $seq) = @_;
if ($seq) {
# check alphabet
if ($seq =~ /[^ACGTUacgtu]/ ) {
warn "Sequence contains illegal characters";
return;
}
else {
$self->{'seq'} = $seq;
}
}
return $self->{'seq'};
}
1;