Class: BisearchEnzimHu::PrimerDesign

Inherits:
Object
  • Object
show all
Defined in:
lib/bisearch_enzim_hu/primer_design.rb

Overview

Primer Design Form (at bisearch.enzim.hu/?m=search)

Constant Summary collapse

URL = 
"http://bisearch.enzim.hu/?m=search"

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(options = {}) ⇒ PrimerDesign

Returns a new instance of PrimerDesign.



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 11

def initialize(options={})
  @agent = Mechanize.new
  @options = default_options.merge options
  @url = @options.delete :url
end

Instance Attribute Details

#chr ⇒ Object (readonly)

Returns the value of attribute chr.



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 9

def chr
  @chr
end

#end_pos ⇒ Object (readonly)

Returns the value of attribute end_pos.



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 9

def end_pos
  @end_pos
end

#form ⇒ Object (readonly)

Returns the value of attribute form.



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 9

def form
  @form
end

#page ⇒ Object (readonly)

Returns the value of attribute page.



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 9

def page
  @page
end

#primers ⇒ Object (readonly)

Returns the value of attribute primers.



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 9

def primers
  @primers
end

#start_pos ⇒ Object (readonly)

Returns the value of attribute start_pos.



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 9

def start_pos
  @start_pos
end

#url ⇒ Object (readonly)

Returns the value of attribute url.



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 9

def url
  @url
end

Instance Method Details

#prepare ⇒ Object 



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 29

def prepare
  # filling form
  @page = @agent.get(@url)
  @form = @page.form
  @options.each_pair do |field_name, value|
    case get_type(field_name)
    when :select # a dropdown
      @form.field_with(name: field_name.to_s).options.find{|e| e.text.downcase=~Regexp.new(value.downcase)}.select
    when :checkbox
      @form.checkbox_with(name: field_name.to_s).send(value ? :check : :uncheck)
    when :radiobutton
      @form.radiobutton_with(name: field_name.to_s).send(value ? :check : :uncheck)
    when :text
      @form.field_with(name: field_name.to_s).value=value
    when :text_area
      @form.field_with(name: field_name.to_s).value=value # same as text
    end
  end
  self
end

#prune ⇒ Object 



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 63

def prune
  indexes_to_remove = []
  puts @primers.inspect
  puts @primers[:output].inspect
  @primers[:output].each_pair do |i, h|
    puts h.inspect
    indexes_to_remove << i if h[:fpcr][:sense][:results].size>1
    indexes_to_remove << i if h[:fpcr][:antisense][:results].size>1
  end
  indexes_to_remove.uniq!
  puts "results to remove: [#{indexes_to_remove.join(', ')}]"
  indexes_to_remove.each{|i| @primers[:output].delete(i)}
end

#search(two_levels = true) ⇒ Object 



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 50

def search(two_levels=true)
  @primers = {}
  puts "---> starting search primers"
  t = Time.now
  page = @agent.submit(@form)
  puts "---> query completed (time: #{Time.now-t}s)"
  @primers[:input] = {chr: @chr, start_pos: @start_pos, end_pos: @end_pos, seq: @options[:seq]}
  res_page = BisearchEnzimHu::L1ResultPage.new(page.body)
  # @primers[:output] = BisearchEnzimHu::L1ResultPage.new(page.body)
  @primers[:output] = res_page.parse(two_levels)
  self
end

#sequence(seq, chr = nil, start_pos = nil) ⇒ Object 



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# File 'lib/bisearch_enzim_hu/primer_design.rb', line 18

def sequence(seq, chr=nil, start_pos=nil)
  @primers = {}
  @chr           = chr
  @start_pos     = start_pos
  @end_pos       = start_pos + seq.size if start_pos
  @options[:seq] = seq
  prepare
  self
end