Class: Bio::Ipcress::PrimerSet

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/ipcress.rb

Overview

A class to represent a pair of primers that will be used by Ipcress to amplify from template DNA in-silico

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(forward_primer, reverse_primer) ⇒ PrimerSet

Returns a new instance of PrimerSet.



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# File 'lib/bio/appl/ipcress.rb', line 111

def initialize(forward_primer, reverse_primer)
  @forward_primer = forward_primer
  @reverse_primer = reverse_primer
end

Instance Attribute Details

#forward_primerObject

Returns the value of attribute forward_primer.



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# File 'lib/bio/appl/ipcress.rb', line 109

def forward_primer
  @forward_primer
end

#reverse_primerObject

Returns the value of attribute reverse_primer.



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# File 'lib/bio/appl/ipcress.rb', line 109

def reverse_primer
  @reverse_primer
end

Instance Method Details

#to_ipcress_format(options = {}) ⇒ Object

To a string in the “ipcress file” format required for ipcress usage



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# File 'lib/bio/appl/ipcress.rb', line 117

def to_ipcress_format(options={})
  options ||= {}
  options[:min_distance] ||= 100
  options[:max_distance] ||= 1000
  "ID1 #{@forward_primer} #{@reverse_primer} #{options[:min_distance]} #{options[:max_distance]}"
end