Bio::SeqFeature::SiRNA
Pair
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Summary
Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA
(SiRNA) oligo pairs
Package variables
No package variables defined.
Inherit
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
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->get_tag_values('rank');
return shift @ranks;
}
else {
$self->throw("Rank not defined for this Pair\n");
return;
}
}} | sub fxGC
{ my ($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->get_tag_values('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;
}
else {
return $self->_get_oligo(1);
}} | sub antisense
{ my ($self, $asoligo) = @_;
if ($asoligo) {
$self->_add_oligo($asoligo, -1) or return;
}
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;
}
1;} | General documentation
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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _