Bio::Seq PrimedSeq
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Package variables
Privates (from "my" definitions)
$static_gff_formatter = undef
Included modules
Bio::RangeI
Inherit
Bio::Seq
Synopsis
  # create a sequence
  my $sequence = "ctagctagctagctagctagctagctagctgatcgtagctagctagct";
  # create left and right primer seqfeatures
  # unfortunately, I haven't created constructors for these yet.
  my $left = Bio::SeqFeature::Primer();
  my $right = Bio::SeqFeature::Primer();
  # now create the PrimedSeq
  $primedseq = new Bio::Seq::PrimedSeq(
                                       -seq => $sequence,
                                       -display_id => "chads_fantastic_sequence",
                                       -LEFT_PRIMER => $left,
                                       -RIGHT_PRIMER => $right,
                                       -TARGET => '513,26'
                                       -PRIMER_PRODUCT_SIZE_RANGE => '100-500'
                                       -PRIMER_FILE_FLAG => '0'
                                       -PRIMER_LIBERAL_BASE => '1'
                                       -PRIMER_NUM_RETURN => '1'
                                       -PRIMER_FIRST_BASE_INDEX => '1'
                                       -PRIMER_EXPLAIN_FLAG => '1'
                                       -PRIMER_PRODUCT_SIZE => '185'
                                       );
  # get the amplified region
  my $amplified_sequence = $primed_seq->get_amplified_sequence();
Description
This module is a slightly glorified capsule containg a primed seqBuence. It was
created to address the fact that a primer is more the a seqfeature and there
need to be ways to represent the primer-sequence complex and the behaviors and
attributes that are associated with the complex.
Methods
_static_gff_formatterDescriptionCode
all_tagsDescriptionCode
display_idDescriptionCode
each_tag_valueDescriptionCode
end()
No description
Code
get_left_primer()
No description
Code
gff_stringDescriptionCode
has_tagDescriptionCode
locationDescriptionCode
newDescriptionCode
primary_tagDescriptionCode
source_tagDescriptionCode
start()
No description
Code
strand()
No description
Code
sub_SeqFeatureDescriptionCode
Methods description
_static_gff_formattercode    nextTop
 Title   : _static_gff_formatter
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :
all_tagscodeprevnextTop
 Title   : all_tags
 Usage   : @tags = $feat->all_tags()
 Function: gives all tags for this feature
 Returns : an array of strings
 Args    : none
display_idcodeprevnextTop
 Title   : display_id
 Usage   : $name = $feat->display_id()
 Function: Returns the human-readable ID of the
           feature for displays.
 Returns : a string
 Args    : none
each_tag_valuecodeprevnextTop
 Title   : each_tag_value
 Usage   : @values = $self->each_tag_value('some_tag')
 Function: 
 Returns : An array comprising the values of the specified tag.
 Args    :
gff_stringcodeprevnextTop
 Title   : gff_string
 Usage   : $str = $feat->gff_string;
           $str = $feat->gff_string($gff_formatter);
 Function: Provides the feature information in GFF format.

           The implementation provided here returns GFF2 by default. If you
           want a different version, supply an object implementing a method
           gff_string() accepting a SeqFeatureI object as argument. E.g., to
           obtain GFF1 format, do the following:

                my $gffio = Bio::Tools::GFF->new(-gff_version => 1);
                $gff1str = $feat->gff_string($gff1io);

 Returns : A string
 Args    : Optionally, an object implementing gff_string().
has_tagcodeprevnextTop
 Title   : has_tag
 Usage   : $tag_exists = $self->has_tag('some_tag')
 Function: 
 Returns : TRUE if the specified tag exists, and FALSE otherwise
 Args    :
locationcodeprevnextTop
 Title   : location
 Usage   : my $location = $seqfeature->location()
 Function: returns a location object suitable for identifying location 
	   of feature on sequence or parent feature  
 Returns : Bio::LocationI object
 Args    : none
newcodeprevnextTop
 Title   : new()
 Usage   : $primed_sequence = new Bio::SeqFeature::Primer( -seq => $sequence,
                                                            -left_primer => $left_primer,
                                                            -right_primer => $right_primer);
 Function: A constructor for an object representing a primed sequence 
 Returns : A Bio::Seq::PrimedSeq object
 Args    : 
     -seq => a Bio::Seq object
     -left_primer => a Bio::SeqFeature::Primer object
     -right_primer => a Bio::SeqFeature::Primer object
     Many other parameters can be included including all of the output
     parameters from the primer3 program.
Developer Notes: This is incomplete and doesn't work. As of ISMB2002 I am working on it.
primary_tagcodeprevnextTop
 Title   : primary_tag
 Usage   : $tag = $feat->primary_tag()
 Function: Returns the primary tag for a feature,
           eg 'exon'
 Returns : a string 
 Args    : none
source_tagcodeprevnextTop
 Title   : source_tag
 Usage   : $tag = $feat->source_tag()
 Function: Returns the source tag for a feature,
           eg, 'genscan' 
 Returns : a string 
 Args    : none
sub_SeqFeaturecodeprevnextTop
 Title   : sub_SeqFeature
 Usage   : @feats = $feat->sub_SeqFeature();
 Function: Returns an array of sub Sequence Features
 Returns : An array
 Args    : none
Methods code
_static_gff_formatterdescriptionprevnextTop
sub _static_gff_formatter {
   my ($self,@args) = @_;

   if( !defined $static_gff_formatter ) {
       $static_gff_formatter = Bio::Tools::GFF->new('-gff_version' => 2);
   }
   return $static_gff_formatter;
}
all_tagsdescriptionprevnextTop
sub all_tags {
   my ($self,@args) = @_;

   $self->throw_not_implemented();
}
display_iddescriptionprevnextTop
sub display_id {
   my ($self,@args) = @_;
  $self->throw_not_implemented();
}
each_tag_valuedescriptionprevnextTop
sub each_tag_value {
   my ($self,@args) = @_;

   $self->throw_not_implemented();
}
end()descriptionprevnextTop
sub end() {
     my $self = shift;
}
get_left_primer()descriptionprevnextTop
sub get_left_primer() {
     my $self = shift;
}
gff_stringdescriptionprevnextTop
sub gff_string {
   my ($self,$formatter) = @_;

   $formatter = $self->_static_gff_formatter unless $formatter;
   return $formatter->gff_string($self);
}

my $static_gff_formatter = undef;
}
has_tagdescriptionprevnextTop
sub has_tag {
   my ($self,@args) = @_;

   $self->throw_not_implemented();
}
locationdescriptionprevnextTop
sub location {
   my ($self) = @_;

   $self->throw_not_implemented();
}


1;
}
newdescriptionprevnextTop
sub new {
     my($class,@args) = @_;
     my %arguments = @args;
     my $self = $class->SUPER::new(@args);
          # these are the absolute minimum components required to make
          # a primedseq
     my $newkey;
     foreach my $key (sort keys %arguments) {
          ($newkey = $key) =~ s/-//;
          $self->{$newkey} = $arguments{$key};
          push @{$self->{arguments}},$newkey;
     }
          # and now the insurance- make sure that things are ok
     if (!$self->{target_sequence} || !$self->{left_primer} || !$self->{right_primer} ) {
          $self->throw("You must provide a target_sequence, left_primer, and right_primer to create this object.");
     }
     if (ref($self->{target_sequence}) ne "Bio::Seq") {
          $self->throw("The target_sequence must be a Bio::Seq to create this object.");
     }
     if (ref($self->{left_primer}) ne "Bio::SeqFeature::Primer" || ref($self->{right_primer}) ne "Bio::SeqFeature::Primer") {
          $self->throw("You must provide a left_primer and right_primer, both as Bio::SeqFeature::Primer to create this object.");
     }
     return $self;
}
primary_tagdescriptionprevnextTop
sub primary_tag {
   my ($self,@args) = @_;

   $self->throw_not_implemented();
}
source_tagdescriptionprevnextTop
sub source_tag {
   my ($self,@args) = @_;

   $self->throw_not_implemented();
}
start()descriptionprevnextTop
sub start() {
     my $self = shift;
}
strand()descriptionprevnextTop
sub strand() {
     my $self = shift;
}
sub_SeqFeaturedescriptionprevnextTop
sub sub_SeqFeature {
   my ($self,@args) = @_;

   $self->throw_not_implemented();
}
General documentation
Bio::Seq::PrimedSeqTop
Bio::Seq::PrimedSeq - A representation of a sequence and two primers flanking a
target region for amplification
FEEDBACKTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org          - General discussion
  http://bio.perl.org/MailList.html             - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
get_left_primerTop
 Title   : get_left_primer();
 Usage   : $left_primer = $primedseq->get_left_primer();
 Function: A getter for the left primer in thie PrimedSeq object.
 Returns : A Bio::SeqFeature::Primer object
 Args    : None.
Bio::RangeI methodsTop
List of interfaces inherited from Bio::RangeI (see Bio::RangeI
for details).
startTop
 Title   : start
 Usage   : $start = $feat->start
 Function: Returns the start coordinate of the feature
 Returns : integer
 Args    : none
Developer Notes:
          This is entirely dependent on the sequence to which this primer is attached!
          I think that there could be trouble if one takes this primer from sequence 1
          and naively place it on sequence 2 without updating this
          ** This is incomplete at this time.
endTop
 Title   : end
 Usage   : $end = $feat->end
 Function: Returns the end coordinate of the feature
 Returns : integer
 Args    : none
Developer Notes:
          ** This is incomplete at this time.
strandTop
 Title   : strand
 Usage   : $strand = $feat->strand()
 Function: Returns strand information, being 1,-1 or 0
 Returns : -1,1 or 0
 Args    : none
Developer Notes:
          ** This is incomplete at this time.
SeqFeatureI specific methodsTop
New method interfaces.
RangeI methodsTop
These methods are inherited from RangeI and can be used
directly from a SeqFeatureI interface. Remember that a
SeqFeature is-a RangeI, and so wherever you see RangeI you
can use a feature ($r in the below documentation).
overlapsTop
  Title   : overlaps
  Usage   : if($feat->overlaps($r)) { do stuff }
            if($feat->overlaps(200)) { do stuff }
  Function: tests if $feat overlaps $r
  Args    : a RangeI to test for overlap with, or a point
  Returns : true if the Range overlaps with the feature, false otherwise
containsTop
  Title   : contains
  Usage   : if($feat->contains($r) { do stuff }
  Function: tests whether $feat totally contains $r
  Args    : a RangeI to test for being contained
  Returns : true if the argument is totaly contained within this range
equalsTop
  Title   : equals
  Usage   : if($feat->equals($r))
  Function: test whether $feat has the same start, end, strand as $r
  Args    : a RangeI to test for equality
  Returns : true if they are describing the same range
Geometrical methodsTop
These methods do things to the geometry of ranges, and return
triplets (start, stop, strand) from which new ranges could be built.
intersectionTop
  Title   : intersection
  Usage   : ($start, $stop, $strand) = $feat->intersection($r)
  Function: gives the range that is contained by both ranges
  Args    : a RangeI to compare this one to
  Returns : nothing if they do not overlap, or the range that they do overlap
unionTop
  Title   : union
  Usage   : ($start, $stop, $strand) = $feat->union($r);
          : ($start, $stop, $strand) = Bio::RangeI->union(@ranges);
  Function: finds the minimal range that contains all of the ranges
  Args    : a range or list of ranges to find the union of
  Returns : the range containing all of the ranges