Bio::SeqFeature::SiRNA
Pair
Summary
Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA
(SiRNA) oligo pairs
Package variables
No package variables defined.
Included modules
Synopsis
use Bio::SeqFeature::SiRNA::Pair;
my $pair = Bio::SeqFeature::SiRNA::Pair->
new( -sense => $bio_seqfeature_sirna_oligo, # strand=1
-antisense => $bio_seqfeature_sirna_oligo, # strand= -1
-primary => 'SiRNA::Pair',
-source_tag => 'Bio::Tools::SiRNA',
-start => 8,
-end => 31,
-rank => 1,
-fxgc => 0.5,
-tag => { note => 'a note' } );
$target_sequence->add_SeqFeature($pair);
Description
Object methods for (complementary) pairs of SiRNA::Oligo objects -
inherits Bio::SeqFeature::Generic. See that package for information
on inherited methods.
DOES NOT include methods for designing SiRNAs -- see
Bio::Tools::SiRNA
None by default.
Methods
Methods description
Title : new
Usage : my $sirna_pair = Bio::SeqFeature::SiRNA::Pair->new();
Purpose : Create a new SiRNA::Pair object
Returns : Bio::Tools::SiRNA object
Args : -start 10
-end 31
-rank 1 # 'Rank' in Tuschl group's rules
-fxgc 0.5 # GC fraction for target sequence
-primary 'SiRNA::Pair', # default value
-source_tag 'Bio::Tools::SiRNA'
-tag { note => 'A note' }
-sense a Bio::SeqFeature::SiRNA::Oligo object
with strand = 1
-antisense a Bio::SeqFeature::SiRNA::Oligo object
with strand = -1
);
Note : SiRNA::Pair objects are typically created by a design
algorithm such as Bio::Tools::SiRNA |
Title : rank
Usage : my $pair_rank = $sirna_pair->rank()
Purpose : Get/set the 'quality rank' for this pair.
See Bio::Tools::SiRNA for a description of ranks.
Returns : scalar
Args : scalar (optional) indicating pair rank |
Title : fxGC
Usage : my $fxGC = $sirna_pair->fxGC();
Purpose : Get/set the fraction of GC for this pair - based on TARGET sequence, not oligos.
Returns : scalar between 0-1
Args : scalar between 0-1 (optional) |
Title : sense
Usage : my $sense_oligo = $sirna_pair->sense()
Purpose : Get/set the SiRNA::Oligo object corresponding to the sense strand
Returns : Bio::SeqFeature::SiRNA::Oligo object
Args : Bio::SeqFeature::SiRNA::Oligo object |
Title : antisense
Usage : my $antisense_oligo = $sirna_pair->antisense()
Purpose : Get/set the SiRNA::Oligo object corresponding to the antisense strand
Returns : Bio::SeqFeature::SiRNA::Oligo object
Args : Bio::SeqFeature::SiRNA::Oligo object |
Methods code
sub new
{ my ($proto, @args) = @_;
my $pkg = ref($proto) || $proto;
my $self = $pkg->SUPER::new();
my %args;
@args{@ARGNAMES} = $self->_rearrange(\@ARGNAMES, @args);
$args{'PRIMARY'} ||= 'SiRNA::Pair';
$args{'PRIMARY'} && $self->primary_tag($args{'PRIMARY'});
$args{'SOURCE_TAG'} && $self->source_tag($args{'SOURCE_TAG'});
$args{'SEQNAME'} && $self->seqname($args{'SEQNAME'});
$args{'ANNOTATION'} && $self->annotation($args{'ANNOTATION'});
$args{'LOCATION'} && $self->location($args{'LOCATION'});
$args{'SENSE'} && $self->sense($args{'SENSE'});
$args{'ANTISENSE'} && $self->antisense($args{'ANTISENSE'});
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'});
defined($args{'RANK'}) && $self->rank($args{'RANK'});
defined($args{'FXGC'}) && $self->fxGC($args{'FXGC'});
if ($args{'TAG'}) {
foreach my $t (keys %{$args{'TAG'}}) {
$self->add_tag_value($t, $args{'TAG'}->{$t});
}
}
return $self;} | sub rank
{ my ($self, $rank) = @_;
if (defined $rank) {
$self->remove_tag('rank') if ( $self->has_tag('rank') );
$self->add_tag_value('rank', $rank);
}
else {
if ($self->has_tag('rank')) {
my @ranks = $self->each_tag_value('rank');
return shift @ranks;
}
else {
$self->throw("Rank not defined for this Pair\n");
return undef;
}
}} | sub fxGC
{ my ($self, $fxGC) = @_;
if (defined $fxGC) {
if ($fxGC =~ /[^.\d]/) {
$self->throw( -class => 'Bio::Root::BadParameter',
-text => "Fraction GC must be a number between 0, 1 - NOT <$fxGC>",
-value => $fxGC
);
}
if ( $fxGC < 0 or $fxGC > 1 ) {
$self->throw( -class => 'Bio::Root::BadParameter',
-text => "Fraction GC must be a number between 0, 1 - NOT <$fxGC>",
-value => $fxGC
);
}
$self->remove_tag('fxGC') if ( $self->has_tag('fxGC') );
$self->add_tag_value('fxGC', $fxGC)
or $self->throw("Unable to set fxGC");
}
else {
if ($self->has_tag('fxGC')) {
my @fxGCs = $self->each_tag_value('fxGC');
return shift @fxGCs;
}
else {
$self->throw("FxGC not defined for this Pair");
}
}} | sub sense
{ my ($self, $soligo) = @_;
if ($soligo) {
$self->_add_oligo($soligo, 1) or return undef;
}
else {
return $self->_get_oligo(1);
}} | sub antisense
{ my ($self, $asoligo) = @_;
if ($asoligo) {
$self->_add_oligo($asoligo, -1) or return undef;
}
else {
return $self->_get_oligo(-1);
}} | sub _add_oligo
{ my ($self, $oligo, $strand) = @_;
unless ($oligo->isa('Bio::SeqFeature::SiRNA::Oligo')) {
$self->throw( -class => 'Bio::Root::BadParameter',
-text => "Oligos must be passed as Bio::SeqFeature::SiRNA::Oligo objects\n");
}
$oligo->strand($strand);
return $self->add_sub_SeqFeature($oligo, 'EXPAND');} | sub _get_oligo
{ my ($self, $strand) = @_;
my $feat;
my @feats = $self->sub_SeqFeature;
foreach $feat (@feats) {
next unless ($feat->primary_tag eq 'SiRNA::Oligo');
next unless ($feat->strand == $strand);
return $feat;
}
return undef;} | General documentation
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/MailList.shtml - About the mailing lists
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:
http://bugzilla.bioperl.org/
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _