Bio::PrimerDesigner::Result(3pm)

Usage

  use Bio::PrimerDesigner;
 
  #  
  # primer3  
  #  
  my $primer3_obj = Bio::PrimerDesigner->new( program => 'primer3 );  
  my $result = $primer3_obj->design( %hash_of_options );
  my $left_primer = $result->left;  
  my @left_primers = $result->left(1..$num_primers);  
 
  #
  # e-PCR -- first make a hash of options from primer3 results
  # then run e-PCR
  #
  my $epcr_obj = Bio::PrimerDesigner->new( program => 'primer3 );
  my $epcr_result = $epcr_obj->design( %hash_of_options );
  my $num_products = $epcr_result->products; 
 
  #
  # one product
  #
  my $first_prod_size = $epcr_result->size;
  my $first_prod_start = $epcr_result->start;
  my $first_prod_stop = $epcr_result->start;  
 
  #
  # more than one product
  #
  my @pcr_product_sizes = ();
  for (1..$num_products) {
      push @pcr_product_sizes, $epcr_result->size;   
  }

Overview

 Bio::PrimerDesigner::Result will autogenerate result access methods
 for for Native Boulder IO keys and Bio::PrimerDesigner keys for
 primer3, e-PCR, isPcr and ipcress.

Methods

keys

 This handles result method calls made via the
 Bio::PrimerDesigner::Result object.  Returns either a scalar or list
 depending on the on the arguments:
  ------------------+------------------------
   Args passed      |  Returns
  ------------------+------------------------
   none                scalar value for set 1
   numeric n           scalar value for set n
   numeric list 1..n   list with n elements
 The aliased output methods (below) return a string when called in a 
 scalar context and a list when called in a list context.  The native 
 primer3 (Boulder IO) keys can also be used.  There are also e-PCR,
 isPcr and ipcress specific methods

Primer3 keys

`•`	left -- left primer sequence
`•`	right -- right primer sequence
`•`	hyb_oligo -- internal oligo sequence
`•`	startleft -- left primer 5' sequence coordinate
`•`	startright -- right primer 5' sequence coordinate
`•`	tmleft -- left primer tm
`•`	tmright -- right primer tm
`•`	qual -- primer pair penalty (Q value)
`•`	lqual -- left primer penalty
`•`	rqual -- right primer penalty
`•`	leftgc -- left primer % gc
`•`	rightgc -- right primer % gc
`•`	lselfany -- left primer self-complementarity (any)
`•`	lselfend -- left primer self-complementarity (end)
`•`	rselfany -- right primer self-complementarity (any)
`•`	rselfend -- right primer self-complementarity (end)
`•`	pairanycomp -- primer pair complementarity (any)
`•`	pairendcomp -- primer pair complementarity (end)
`•`	lendstab -- left primer end stability
`•`	rendstab -- right primer end stability
`•`	amplicon -- amplified PCR product

Other keys

`•`	products -- number of PCR products
`•`	size -- product size
`•`	start -- product start coordinate
`•`	stop -- product stop coordinate
`•`	end -- synonymous with stop
`•`	strand -- strand of product relative to the ref. sequence (isPCR, ipcress)
`•`	amplicon -- returns the PCR product (isPCR only)

Releases

8 releases since Debian 6.0 (Squeeze); the text changed 4 times.